• Asian Pacific Journal of Cancer Prevention
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• v.14 no.11
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• pp.6403-6409
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• 2013

Purpose: Biallelic germline variants of the 8-hydroxyguanine (8-OG) repair gene MYH have been associated with colorectal neoplasms that display somatic $G:C{\rightarrow}T:A$ transversions. However, the effect of single germline variants has not been widely studied, prompting the present investigation of monoallelic MYH variants and susceptibility to sporadic colorectal cancer (CRC) in a Chinese population. Patients and Methods: Between January 2006 and December 2012, 400 cases of sporadic CRC and 600 age- and sex-matched normal blood donors were screened randomly for 7 potentially pathogenic germline MYH exons using genetic testing technology. Variants of heterozygosity at the MYH locus were assessed in both sporadic cancer patients and healthy controls. Univariate and multivariate analyses were performed to determine risk factors for cancer onset. Results: Five monoallelic single nucleotide polymorphisms (SNPs) were identified in the 7 exon regions of MYH, which were detected in 75 (18.75%) of 400 CRC patients as well as 42 (7%) of 600 normal controls. The region of exon 1 proved to be a linked polymorphic region for the first time, a triple linked variant including exon 1-316 $G{\rightarrow}A$, exon 1-292 $G{\rightarrow}A$ and intron 1+11 $C{\rightarrow}T$, being identified in 13 CRC patients and 2 normal blood donors. A variant of base replacement, intron 10-2 $A{\rightarrow}G$, was identified in the exon 10 region in 21 cases and 7 controls, while a similar type of variant in the exon 13 region, intron 13+12 $C{\rightarrow}T$, was identified in 8 cases and 6 controls. Not the only but a newly missense variant in the present study, p. V463E (Exon 14+74 $T{\rightarrow}A$), was identified in exon 14 in 6 patients and 1 normal control. In exon 16, nt. 1678-80 del GTT with loss of heterozygosity (LOH) was identified in 27 CRC cases and 26 controls. There was no Y165C in exon 7 or G382D in exon 14, the hot-spot variants which have been reported most frequently in Caucasian studies. After univariate analysis and multivariate analysis, the linked variant in exon 1 region (p=0.002), intron 10-2 $A{\rightarrow}G$ (p=0.004) and p. V463E (p=0.036) in the MYH gene were selected as 3 independent risk factors for CRC. Conclusions: According to these results, the linked variant in Exon 1 region, Intron 10-2 $A{\rightarrow}G$ of base replacement and p. V463E of missense variant, the 3 heterozygosity variants of MYH gene in a Chinese population, may relate to the susceptibility to sporadic CRC. Lack of the hot-spot variants of Caucasians in the present study may due to the ethnic difference in MYH gene.

• Korean Journal of Food Science and Technology
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• v.50 no.5
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• pp.480-485
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• 2018

In this study, to identify single nucleotide polymorphisms (SNPs) associated with meat quality in Berkshire pigs, we performed RNA sequencing. A non-synonymous SNP (nsSNP) in the Complement component 9 (C9) gene was identified, and the association between meat quality traits and the C9 genotype was analyzed. The nsSNP in the C9 gene was located at c.942 G>T. In the dominant model, significant associations were observed between the SNP and meat quality traits such as CIE L, collagen content, moisture level, and $pH_{24h}$, whereas in the co-dominant model, significant associations were observed between the SNP and CIE L, collagen content, and protein content. In the recessive model, a significant association between the C9 genotype and the collagen content was observed. In addition, we identified the significant relationship between the C9 genotype and meat quality according to sex. These results indicate that the C9 SNP can be used as a genetic marker for improving pork quality.

• Genomics & Informatics
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• v.16 no.2
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• pp.36-41
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• 2018

Kawasaki disease (KD) is an acute febrile vasculitis predominately affecting infants and children. The dominant incidence age of KD is from 6 months to 5 years of age, and the incidence is unusual in those younger than 6 months and older than 5 years of age. We tried to identify genetic variants specifically associated with KD in patients younger than 6 months or older than 5 years of age. We performed an age-stratified genome-wide association study using the Illumina HumanOmni1-Quad BeadChip data (296 cases vs. 1,000 controls) and a replication study (1,360 cases vs. 3,553 controls) in the Korean population. Among 26 candidate single nucleotide polymorphisms (SNPs) tested in replication study, only a rare nonsynonymous SNP (rs4365796: c.1106C>T, p.Thr369Met) in the lymphoid enhancer binding factor 1 (LEF1) gene was very significantly associated with KD in patients younger than 6 months of age (odds ratio [OR], 3.07; $p_{combined}=1.10{\times}10^{-5}$), whereas no association of the same SNP was observed in any other age group of KD patients. The same SNP (rs4365796) in the LEF1 gene showed the same direction of risk effect in Japanese KD patients younger than 6 months of age, although the effect was not statistically significant (OR, 1.42; p = 0.397). This result indicates that the LEF1 gene may play an important role as a susceptibility gene specifically affecting KD patients younger than 6 months of age.

• Korean Journal of Poultry Science
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• v.40 no.2
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• pp.139-145
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• 2013

There are several loci controlling the feather color of birds, of which one of the most studied is Extended black (E) encoding the melanocortin 1-receptor (MC1R). Mutations in this gene affect the relative distribution of eumelanin, phaeomelanin. The association of feather color and sequence polymorphism in the melanocortin 1-receptor (MC1R) gene was investigated using Korean native chicken H breed (H_PL) and 'Woorimatdag' commercial chickens (Woorimatdag_CC). In order to correlate gene mutation to Korean native chicken feather color, single nucleotide polymorphism (SNP) from MC1R gene sequence were investigated. A total of 307 birds from H_PL and Woorimatdag_CC were used. H_PL have black, black-brown feather color and Woorimatdag_CC have black with brown spots or brown with black spots. There are 6 SNPs in MC1R gene, locus T69C, C212T, A274G, G376A, G636A, T637C. 3 SNPs are nonsynonymous that change amino acid. But it is difficult to find correlation of feather color and polymorphisms. It will be needed to increase the population of Korean native chicken H breed and correlation analysis of genetic variation with feather colors.

• Clinical and Experimental Pediatrics
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• v.53 no.4
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• pp.548-553
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• 2010

Purpose : IgA nephropathy (IgAN) is the most commonly occurring form of chronic glomerulonephritis in pediatric cases. Human leukocyte antigen (HLA) genes have been implicated in various inflammatory and autoimmune diseases. The present study was conducted to investigate the association between 2 single nucleotide polymorphisms (SNPs) of the HLA-G gene and childhood IgAN. Methods : The authors analyzed and compared $HLA-G$ gene SNPs (rs1736936 and rs2735022) in 174 patients with childhood IgAN and in 438 healthy controls. In addition, IgAN patients were dichotomized and compared with respect to proteinuria (< and >$4mg/m^2/hour$), the presence or absence of podocyte foot process effacement, and the presence of pathologically early and advanced disease markers such as interstitial fibrosis, tubular atrophy, or global sclerosis. Results : No significant SNP frequency differences were observed for the $HLA-G$ gene between IgAN patients and the control group. Moreover, no significantly associated SNP was observed with the presence of proteinuria, podocyte foot process effacement, or pathologically advanced markers. However, the haplotype, composed of rs1736936 and rs2735022, showed a significant association with the susceptibility to develop childhood IgAN (haplotype T/C: dominant model, $P$=0.049; haplotype C/T: recessive model, $P$=0.030). Conclusion : Our results indicate that rs1736936 and rs2735022 as the $HLA-G$ gene promoter haplotype might be associated with the susceptibility to develop childhood IgAN in the Korean population.

• Journal of Life Science
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• v.26 no.11
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• pp.1232-1236
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• 2016

Mitochondrial calcium uptake 1 (MICU1) including two canonical EF hands, located in the mitochondrial inner membrane, is known to play a crucial role in the calcium uptake in mitochondria. Mitochondrial calcium uptake in muscular cells is related to post mortem shortening by calcium release from muscles. Therefore, the porcine MICU1 gene has been estimated as a genetic candidate for meat quality traits. In this study, variations on the exonic regions of the porcine MICU1 gene were investigated by sequencing cDNAs and tested for their association with meat quality traits. A total of 667 Berkshire heads (347 sows and 320 castrated boars) were used for this association test. Three SNPs were detected on the 3' untranslated region (UTR) of the porcine MICU1 gene. SNP1 (c.*136G>A) was associated with drip loss (p=0.017) and intramuscular fat content (p=0.039). In addition, SNP2 (c.*222G>A) and SNP3 (c.*485G>A) were associated with drip loss (p=0.018) and intramuscular fat content (p<0.001), respectively. In conclusion, it was verified that three variations on the 3' UTR of the porcine MICU1 gene were significantly associated with meat quality traits. It was also suggested that molecular biological analyses are needed to validate the function of variations on the 3 UTR of the porcine MICU1 gene.