• Asian Pacific Journal of Cancer Prevention
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• v.15 no.24
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• pp.10719-10722
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• 2015

Several lines of evidence suggest that MUC5AC genetic polymorphisms might confer susceptibility to H. pylori infection and therefore gastric cancer risk. We here assessed the association of common polymorphisms in the MUC5AC gene with H. pylori seroprevalence using an LD-based tagSNP approach in a north-western Chinese Han population. A total of 12 tagSNPs were successfully genotyped among 281 unrelated ethnic Han Chinese who had no cancer history, and no identifiable gastric disease or genetic disease. No significant association between any alleles, genotypes or haplotypes and H. pylori seroprevalence was observed. Our results suggest that common genetic variations in MUC5AC gene might not make a major contribution to the risk of H. pylori infection.

• Journal of Animal Science and Technology
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• v.56 no.8
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• pp.28.1-28.6
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• 2014

This study was conducted to estimate the effective population size using SNPs data of 240 Jeju horses that had raced at the Jeju racing park. Of the total 61,746 genotyped autosomal SNPs, 17,320 (28.1%) SNPs (missing genotype rate of >10%, minor allele frequency of <0.05 and Hardy-Weinberg equilibrium test P-value of < $10^{-6}$) were excluded after quality control processes. SNPs on the X and Y chromosomes and genotyped individuals with missing genotype rate over 10% were also excluded, and finally, 44,426 (71.9%) SNPs were selected and used for the analysis. The measures of the LD, square of correlation coefficient ($r^2$) between SNP pairs, were calculated for each allele and the effective population size was determined based on $r^2$ measures. The polymorphism information contents (PIC) and expected heterozygosity (HE) were 0.27 and 0.34, respectively. In LD, the most rapid decline was observed over the first 1 Mb. But $r^2$ decreased more slowly with increasing distance and was constant after 2 Mb of distance and the decline was almost linear with log-transformed distance. The average $r^2$ between adjacent SNP pairs ranged from 0.20 to 0.31 in each chromosome and whole average was 0.26, while the whole average $r^2$ between all SNP pairs was 0.02. We observed an initial pattern of decreasing $N_e$ and estimated values were closer to 41 at 1 ~ 5 generations ago. The effective population size (41 heads) estimated in this study seems to be large considering Jeju horse's population size (about 2,000 heads), but it should be interpreted with caution because of the technical limitations of the methods and sample size.

• The Korean Journal of Applied Statistics
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• v.18 no.2
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• pp.297-310
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• 2005

In this study we investigate the association between the haplotype block of 4 SNPs in ACE genes and hypertension with a case-control dataset of size of 277 and 40 families data collected from Kangwha studies. To this end we perform a haplotype-based case-control association study and a haplotype-based TDT study. We do the same analysis with tag-SNPs that can identify the haplotype block. Through a cladogram analysis we make the evolution-tree of haplotypes and then classify the haplotypes into a few clades by collecting haplotypes exposed to the disease to the same extent. We also discuss the association between these clades and hypertension.

• Journal of the Korean Data and Information Science Society
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• v.28 no.3
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• pp.597-604
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• 2017

In this study, we investigated the genetic characteristics and the effective population size of domestic dairy cattle using 42,201 SNPs for 923 heads of Holstein cattle. The estimate for the average linkage disequilibrium ($r^2$) among the adjacent SNPs by chromosome was 0.22, and it was highest (0.26) in chromosome 14 and lowest (0.17) in chromosome 27. When the physical distance among SNPs was less than 25Kb, the estimate for the average $r^2$ was $0.31{\pm}0.33$ and it was markedly decreased as the physical distance increased. When the physical distance among SNPs was larger than 25Mb, the estimate for the average $r^2$ was 0.04, and it decreased by 0.27 (87.1%) compared with case of physical distance of less than 25Kb. There was a trend that the effective population size in Holstein dairy cattle decreased over generations and the estimate for the effective population size in the first 5 generations (1~5th generation) was 110 heads.

• Asian Pacific Journal of Cancer Prevention
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• v.14 no.12
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• pp.7355-7358
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• 2013

Several lines of evidence support the notion that MUC1 is often aberrantly expressed in gastric cancer, and it is a ligand for Helicobacter pylori. Genetic variation in MUC1 gene may confer susceptibility to H. pylori infection and gastric cancer. We assessed the association of common polymorphisms in MUC1 gene with H. pylori infection and non-cardia gastric cancer using an LD-based tag SNP approach in north-western Chinese Han population. A total of four SNPs were successfully genotyped among 288 patients with non-cardia gastric cancer and 281 age- and sex-matched controls. None of the tested SNPs was associated with H. pylori infection. SNP rs9426886 was associated with a decreased risk of non-cardia gastric cancer, but lost significance after adjustment for multiple testing. Overall, our data indicated that common genetic variations in MUC1 gene might not make a major contribution to the risk of H. pylori infection and non-cardia gastric cancer in our studied population.

• Journal of Plant Biotechnology
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• v.5 no.4
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• pp.193-195
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• 2003

A major goal of agricultural biotechnology is the discovery of genes or genetic loci which are associated with characteristics beneficial to crop production. This knowledge of genetic loci may then be applied to improve crop breeding. Agriculturally important genes may also benefit crop production through transgenic technologies. Recent years have seen an application of high throughput technologies to agricultural biotechnology leading to the production of large amounts of genomic data. The challenge today is the effective structuring of this data to permit researchers to search, filter and importantly, make robust associations within a wide variety of datasets. At the Plant Biotechnology Centre, Primary Industries Research Victoria in Melbourne, Australia, we have developed a series of tools and computational pipelines to assist in the processing and structuring of genomic data to aid its application to agricultural biotechnology resear-ch. These tools include a sequence database, ASTRA, for the processing and annotation of expressed sequence tag data. Tools have also been developed for the discovery of simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) molecular markers from large sequence datasets. Application of these tools to Brassica research has assisted in the production of genetic and comparative physical maps as well as candidate gene discovery for a range of agronomically important traits.

• Asian-Australasian Journal of Animal Sciences
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• v.32 no.4
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• pp.485-493
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• 2019

Objective: This study was undertaken to investigate the genetic characteristics of Berkshire (BS), Landrace (LR), and Yorkshire (YS) pig breeds raised in the Great Grandparents pig farms using the single nucleotide polymorphisms (SNP) information. Methods: A total of 25,921 common SNP genotype markers in three pig breeds were used to estimate the expected heterozygosity ($H_E$), polymorphism information content, F-statistics ($F_{ST}$), linkage disequilibrium (LD) and effective population size ($N_e$). Results: The chromosome-wise distribution of $F_{ST}$ in BS, LR, and YS populations were within the range of 0-0.36, and the average $F_{ST}$ value was estimated to be $0.07{\pm}0.06$. This result indicated some level of genetic segregation. An average LD ($r^2$) for the BS, LR, and YS breeds was estimated to be approximately 0.41. This study also found an average $N_e$ of 19.9 (BS), 31.4 (LR), and 34.1 (YS) over the last 5th generations. The effective population size for the BS, LR, and YS breeds decreased at a consistent rate from 50th to 10th generations ago. With a relatively faster $N_e$ decline rate in the past 10th generations, there exists possible evidence for intensive selection practices in pigs in the recent past. Conclusion: To develop customized chips for the genomic selection of various breeds, it is important to select and utilize SNP based on the genetic characteristics of each breed. Since the improvement efficiency of breed pigs increases sharply by the population size, it is important to increase test units for the improvement and it is desirable to establish the pig improvement network system to expand the unit of breed pig improvement through the genetic connection among breed pig farms.

• Journal of Life Science
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• v.17 no.12
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• pp.1622-1626
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• 2007

This study was conducted to identify useful single nucleotide polymorphisms (SNPs) and determine their association with economically important traits in pig population. Four candidate gene analyses have identified important chromosomal regions and major genes associcated whit economic traits of the pig. For application of the chromosomal information to the pig industry using DNA technology, SNP markers were developed by comparative re-sequencing of polymerase chain reaction (PCR) products of 4 candidate genes (CSF2, IL4, MYOD, RIP140). PCR restriction fragment length polymorphism (PCR-RFLP) assays were developed for these 4 SNPs and used to genotype Berkshire pig populations in Korea.

• Genomics & Informatics
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• v.5 no.4
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• pp.152-160
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• 2007

Most common diseases are caused by multiple genetic and environmental factors. Among the genetic factors, single nucleotide polymorphisms (SNPs) are common DNA sequence variations in individuals and can serve as important genetic markers. Recently, investigations of gene-based and whole genome-based SNPs have been applied to association studies for marker discovery. However, SNPs are so population-specific that the association needs to be verified. Fifty-five genes and 384 SNPs were selected based on association with disease. Genotypes of 337 SNPs in candidate genes were determined using Illumina Sentrix Array Matrix (SAM) chips by an allele-specific extension method in 364 unrelated Korean individuals. Allelic frequencies of SNPs were compared with those of other populations obtained from the International HapMap database. Minor allele frequencies, linkage disequilibrium blocks, tagSNPs, and haplotypes of functional candidate SNPs in 55 genetic disease-associated genes were provided. Our data may provide useful information for the selection of genetic markers for gene-based genetic disease-association studies of the Korean population.

• Asian-Australasian Journal of Animal Sciences
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• v.27 no.9
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• pp.1236-1243
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• 2014

Genetics is important for breeding and selection of horses but there is a lack of well-established horse-related browsers or databases. In order to better understand horses, more variants and other integrated information are needed. Thus, we construct a horse genomic variants database including expression and other information. Horse Single Nucleotide Polymorphism and Expression Database (HSDB) (http://snugenome2.snu.ac.kr/HSDB) provides the number of unexplored genomic variants still remaining to be identified in the horse genome including rare variants by using population genome sequences of eighteen horses and RNA-seq of four horses. The identified single nucleotide polymorphisms (SNPs) were confirmed by comparing them with SNP chip data and variants of RNA-seq, which showed a concordance level of 99.02% and 96.6%, respectively. Moreover, the database provides the genomic variants with their corresponding transcriptional profiles from the same individuals to help understand the functional aspects of these variants. The database will contribute to genetic improvement and breeding strategies of Thoroughbreds.