• Clinical and Experimental Pediatrics
• /
• v.46 no.4
• /
• pp.340-344
• /
• 2003

Purpose : We evaluated allele frequencies and distribution of surfactant protein A2(SP-A2) in Korean neonates in order to estimate the prevalence of RDS, to find out new SP-A alleles, and to establish new steroid therapy. Methods : Genomic DNA was extracted from 71 neonates and served as a template in PCR for genotype analysis. SP-A gene-specific amplications and gene-specific allele determinations were performed using PCR-cRFLP methods. Results : The distribution for the alleles of the SP-A2 gene in the study population was 1A, $1A^0$, $1A^1$, $1A^2$, $1A^3$, $1A^5$, $1A^6$, $1A^7$, $1A^8$, $1A^9$, $1A^{11}$, $1A^{12}$. The specific frequencies for the alleles of the SP-A2 gene in the study population were : 1A=11.3%, $1A^0=38%$, $1A^1=12.7%$, $1A^2=9.2%$, $1A^5=15.5%$, $1A^7=2.9%$, $1A^8=4.9%$, $1A^9=2.2%$, others=3.3%. Conclusion : The frequency of $1A^0$ was higher than the other SP-A2 alleles in Korean neonates. This finding suggests that the prevalence of RDS in Korea may be low compared with other countries. However, this finding also suggests that Korean neonates have a high risk of infection.

• Clinical and Experimental Pediatrics
• /
• v.45 no.12
• /
• pp.1497-1502
• /
• 2002

Purpose : We evaluated allele frequencies and distribution of surfactant protein A1(SP-A1) in Korean neonates in order to estimate prevalence of RDS to find out new SP-A alleles, and to establish new steroid therapy. Methods : Genomic DNA was extracted from 100 neonates and served as a template in PCR for genotype analysis. SP-A gene-specific amplications and gene-specific allele determinations were performed using PCR-RFLP methods. Results : The distribution for the alleles of the SP-A1 gene in the study population were 6A, $6A^2$, $6A^3$, $6A^4$, $6A^8$, $6A^9$, $6A^{10}$, $6A^{11}$, $6A^{12}$, $6A^{13}$, $6A^{14}$, $6A^{15}$, $6A^{16}$, $6A^{17}$, $6A^{18}$, $6A^{20}$. The specific frequencies for the alleles of the SP-A1 gene in the study population were : $6A^2=21%$, $6A^3=45%$, $6A^4=11%$, $6A^8=9%$, $6A^{14}=8%$. Conclusion : The frequency of $6A^3$ was higher than the other SP-A1 alleles in Korean neonates. This finding suggests that the prevalence of RDS in Korea may be low compared with other countries. However, this finding also suggests that Korean neonates have a high risk of infection.

• Journal of Animal Science and Technology
• /
• v.55 no.3
• /
• pp.165-171
• /
• 2013

Genomic relationship matrix (GRM) was constructed using whole genome SNP markers of swine and genomic breeding value was estimated by substitution of the numerator relationship matrix (NRM) based on pedigree information to GRM. Genotypes of 40,706 SNP markers from 448 pure Landrace pigs were used in this study and five kinds of GRM construction methods, G05, GMF, GOF, $GOF^*$ and GN, were compared with each other and with NRM. Coefficients of GOF considering each of observed allele frequencies showed the lowest deviation with coefficients of NRM and as coefficients of GMF considering the average minor allele frequency showed huge deviation from coefficients of NRM, movement of mean was expected by methods of allele frequency consideration. All GRM construction methods, except for $GOF^*$, showed normally distributed Mendelian sampling. As the result of breeding value (BV) estimation for days to 90 kg (D90KG) and average back-fat thickness (ABF) using NRM and GRM, correlation between BV of NRM and GRM was the highest by GOF and as genetic variance was overestimated by $GOF^*$, it was confirmed that scale of GRM is closely related with estimation of genetic variance. With the same amount of phenotype information, accuracy of BV based on genomic information was higher than BV based on pedigree information and these symptoms were more obvious for ABF then D90KG. Genetic evaluation of animal using relationship matrix by genomic information could be useful when there is lack of phenotype or relationship and prediction of BV for young animals without phenotype.

• Asian-Australasian Journal of Animal Sciences
• /
• v.17 no.10
• /
• pp.1366-1368
• /
• 2004

The Mafriwal dairy cattle was developed to meet the demands of the Malaysian dairy Industry. Although there are reports on its production and reproductive performance, there has been no work on its molecular characterization. This study was conducted to characterize the Mafriwal dairy cattle using microsatellite markers. Fifty two microsatellite loci were analysed for forty Mafriwal dairy cows kept at Institut Haiwan Kluang, Malaysia. The study showed two microsatellite loci to be monomorphic. Allele frequencies for the polymorphic loci ranged from 0.01 to 0.31. Genotype frequencies ranged from 0.03 to 0.33. The mean overall heterozygosity was 0.79. All polymorphic microsatellite loci deviated significantly (p<0.01) from Hardy-Weinberg equilibrium. The Mafriwal dairy cattle showed high genetic variability despite being a nucleus herd and artificial insemination being practiced.

• Asian-Australasian Journal of Animal Sciences
• /
• v.22 no.1
• /
• pp.1-6
• /
• 2009

Genetic variability is an important component in the ability of populations to adapt in the face of environmental change. Severe human impacts reduced Muzzafarnagri sheep of India from 500,000 in 1972 to 10,989 in 1973-74. Here we report for the first time the effect of this population decline on levels of genetic variability at 13 FAO recommended ovine microsatellite loci and contrast levels of variability to that in a breed from the same geographical region, which differed in numbers, by an order of magnitude (Marwari sheep). Of the 13 loci, 100% were polymorphic in both breeds. A high degree of genetic variation was observed within populations in terms of both allele diversity (number of alleles per locus, >4) and gene diversity (expected heterozygosity, >0.5), which implied that there is still a substantial amount of genetic diversity at the nuclear loci in a declining population. Nevertheless, overall low number of alleles per locus and relatively less abundance of low frequency alleles in Muzzafarnagri sheep suggested that genetic variability has been comparatively reduced in this population. Bottleneck analysis indicated that a genetic bottleneck did not occur during the most recent decline. In addition, we found that the differentiation among populations was moderate ($F_{ST}$= 11.8%). This study on assessment of genetic effects of the population declines in ovines is a step towards identification of genetically impoverished or healthy populations, which could prove to be a useful tool to facilitate conservation planning in this important species of small ruminants.

• Asian Pacific Journal of Cancer Prevention
• /
• v.13 no.11
• /
• pp.5691-5694
• /
• 2012

Ectopic expression of CDX2 in the stomach is closely associated with chronic Helicobacter pylori (H. pylori) infection and intestinal metaplasia. Whether CDX2 has tumor suppression or tumorigenesis potential remains to be elucidated. In this study, we investigated the association between the CDX2 G543C polymorphism (silent mutation) and the risk for H. pylori-induced gastric atrophy and cancer as well as H. pylori infection, using 454 Japanese subjects undergoing a health checkup and 202 gastric cancer patients. The frequency of the minor allele was the same as previously reported in China, but different from that reported in England. CDX2 G543C was not associated with risk of H. pylori infection, gastric atrophy, or gastric cancer, although the point estimate for non-cardiac differentiated gastric cancer as compared to controls with gastric atrophy was 2.22 (95%CI=0.17-29.4). In conclusion, our results indicate that the CDX2 G543C polymorphism is unlikely to affect the H. pylori infection-gastric atrophy-gastric cancer sequence.

• Genomics & Informatics
• /
• v.15 no.4
• /
• pp.136-141
• /
• 2017

Accurate detection of genomic alterations, especially druggable hotspot mutations in tumors, has become an essential part of precision medicine. With targeted sequencing, we can obtain deeper coverage of reads and handle data more easily with a relatively lower cost and less time than whole-exome or whole-genome sequencing. Recently, we designed a customized gene panel for targeted sequencing of major solid cancers. In this study, we aimed to validate its performance. The cancer panel targets 95 cancer-related genes. In terms of the limit of detection, more than 86% of target mutations with a mutant allele frequency (MAF) <1% can be identified, and any mutation with >3% MAF can be detected. When we applied this system for the analysis of Acrometrix Oncology Hotspot Control DNA, which contains more than 500 COSMIC mutations across 53 genes, 99% of the expected mutations were robustly detected. We also confirmed the high reproducibility of the detection of mutations in multiple independent analyses. When we explored copy number alterations (CNAs), the expected CNAs were successfully detected, and this result was confirmed by target-specific genomic quantitative polymerase chain reaction. Taken together, these results support the reliability and accuracy of our cancer panel in detecting mutations. This panel could be useful for key mutation profiling research in solid tumors and clinical translation.

• Genomics & Informatics
• /
• v.18 no.1
• /
• pp.4.1-4.6
• /
• 2020

Transposable elements (TEs) constitute approximately half of Bovine genome. They can be a powerful species-specific marker without regression mutations by the structure variation (SV) at the time of genomic evolution. In a previous study, we identified the Hanwoo-specific SV that was generated by a TE-association deletion event using traditional PCR method and Sanger sequencing validation. It could be used as a molecular marker to distinguish different cattle breeds (i.e., Hanwoo vs. Holstein). However, PCR is defective with various final copy quantifications from every sample. Thus, we applied to the droplet digital PCR (ddPCR) platform for accurate quantitative detection of the Hanwoo-specific SV. Although samples have low allele frequency variation within Hanwoo population, ddPCR could perform high sensitive detection with absolute quantification. We aimed to use ddPCR for more accurate quantification than PCR. We suggest that the ddPCR platform is applicable for the quantitative evaluation of molecular markers.

• The Journal of Korea Assosiation for Disability and Oral Health
• /
• v.4 no.1
• /
• pp.12-16
• /
• 2008

Williams syndrome is a rare genetic disorder with a frequency of one per 20,000~50,000 live births. It is caused by a deletion of one elastin allele located within chromosome subunit 7q11.23(long arm). This syndrome is frequently accompanied by disorders such as congenital heart disease, facial anomalies, mental retardation, and so on. The characteristic facial appearance includes full lips, rounded cheeks, broad forehead, periorbital fullness, flattened bridge of nose, small nose with anteverted nostril, long filtrum and low-set ears. In oral features, hypodontia, high prevalence of dental caries, microdontia, enamel hypoplasia, delayed eruption, and malocclusions have been found. Most adult patients with Williams syndrome lack social adaptability and lead seclusive lives, however, young patients are rather very friendly and talkative, and seem smarter than their actual intellectual quotients. They also tend to favor staying with grown-ups rather than mixing with their peers, and tend to present problematic temper tantrum during dental treatment.

• Korean Journal of Biological Psychiatry
• /
• v.4 no.2
• /
• pp.234-236
• /
• 1997

Though initial report from Japan showed positive association of schizophrenia with dinucleotide repeat polymorphism in the NT-3 gene, subsequent studies showed mixed results. Therefore we conducted a replication study with Korean schizophrenics and matched controls who share similar ethnic background with Japanese population. The frequency of allele of dinucleotide repeat at 147 base pairs in the NT-3 gene was slightly increased, however, failed to reach statistical significance(${\chi}^2$=1.884, df=1, p<0.170) between the two groups. These findings do not support an association of NT-3 gene polymorphism with schizophrenia in Korean sample.