• Asian Pacific Journal of Cancer Prevention
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• v.17 no.3
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• pp.1583-1588
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• 2016

Background: Polycystic ovary syndrome (PCOS) is considered to be a multifactorial disorder resulting from the interaction of several predisposing and protective genetic variants. PCOS is associated with low-grade chronic inflammation. Elevated levels of inflammatory markers including intercellular adhesion molecule-1 (ICAM-1) are demonstrated in women with PCOS. Recent evidence indicates a significant linkage between a locus on chromosome 19p13 and multifactorial diseases that have an inflammatory component. The aim of the study was to assess the possible association of Gly241Arg polymorphism of ICAM-1 gene located on chromosome 19p13 in determining risk of PCOS in Kashmiri women. Materials and Methods: Gly241Arg SNP in DNA from peripheral blood leukocytes of 220 PCOS cases and 220 age matched non-PCOS healthy controls was analysed using allel specific PCR. Results: The genotype and allele frequency distributions of Gly241Arg SNP showed insignificant difference between the PCOS cases and control women, indicating no role of this SNP in PCOS susceptibility. The odds ratio for Arg/Arg genotype was 0.87 (95% CI=0.32-2.3) [P=0.79], for Gly/Arg genotype was 0.98 (95% CI= 0.66-1.47) [P=1] and for Arg/Arg+Gly/Arg genotype was 0.97 (95% CI=0.65-1.45) [P=0.92]. The genotypic frequencies of ICAM-1codon 241 showed statistically insignificant difference between cases and controls (${\chi}^2=0.07$; p=0.96) Nor the studied polymorphism was found to affect clinical and laboratory parameters significantly. Conclusions: Although Gly241Arg polymorphism have not shown significant association with PCOS. Further, specifically designed studies on large cohorts are required to conclusively establish any role of ICAM-1 gene polymorphisms in PCOS in our study.

• Genomics & Informatics
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• v.21 no.4
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• pp.47.1-47.12
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• 2023

Silver barb (Barbonymus gonionotus) is among the most economically important freshwater fish species in Thailand. It ranks fourth in economic value and third in production weight for fisheries and culture in Thailand. An XX/XY sex-determination system based on gynogenesis was previously reported for this fish. In this study, the molecular basis underlying the sex-determination system was further investigated. Genome-wide single-nucleotide polymorphism data were generated for 32 captive-bred silver barb individuals, previously scored by phenotypic sex, to identify sex-linked regions associated with sex determination. Sixty-three male-linked loci, indicating putative XY chromosomes, were identified. Male-specific loci were not observed, which indicates that the putative Y chromosome is young and the sex determination region is cryptic. A homology search revealed that most male-linked loci were homologous to the Mariner/Tc1 and Gypsy transposable elements and are probably the remnants of an initial accumulation of repeats on the Y chromosome from the early stages of sex chromosome differentiation. This research provides convincing insights into the mechanism of sex determination and reveals the potential sex determination regions in silver barb. The study provides the basic data necessary for increasing the commercial value of silver barbs through genetic improvements.

• Korean Journal of Biological Psychiatry
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• v.3 no.2
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• pp.162-169
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• 1996

An association study with korean schizophrenic patients(N=75) and normal controls(N=87) was performed to find the relationship between D6S274 polymorphism and schizophrenia using polymerase chain reaction. Nine different alleles of a dinucleotide polymorphism on D6S273 locus were observed in both group. When we compared the frequencies of alleles between schizophrenics and normal controls, there was no significant difference between two groups. To increase homogeneity of schizophrenic group, we divided schizophrenic group by clinical phenotypes such as DSM-IV diagnostic subtype, family history, negative and positive symptoms(PANSS), soft neurologic signs(NES-K). Then we compared the frequencies of alleles among subgroups of clinical phenotypes. there was only significant difference between two subgroups on soft neurologic signs(p<0.05). Although our findings fail to provide on evidence of association between schizophrenia and D6S274 locus, follow-up investigation of this locus may be needed in homogeneous subtypes of schizophrenia and schizophrenic pedigrees.

• Proceedings of the Korean Information Science Society Conference
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• 2004.10b
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• pp.253-255
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• 2004

인간(human)에게 나타나는 다양성(variation)은 인체의 유전체(genome) 안에서 발생된 SNP(Single Nucleotide Polymorphism)에 의해 나타난다고 알려져 있다. 유전체내의 SNP과 다양성에 대한 연관 연구(Associate study)를 할 때에 약 30여 억 개로 추정되는 염기서열(DNA sequence)물 모두 분석한다면 많은 비용과 시간을 필요로 할 것이다. 이런 비용과 시간을 줄이기 위친 적은 수의 대표 SNP(=tagSNP)을 찾는 연구가 현재 진행 중이다. 우리는 LD계수｜D;｜을 block 분할에 이용하여 생물학적인 의미를 부여한 후, 전산적인 최적해를 찾는 접근을 이용했다. 또한, 기존 연구에서는 large-scale data에 대한 처리가 불가능해서 chromosome의 일부분의 데이터에 대해서안 분석이 시도되었다. 더욱 광범위한 분석을 위해서 chromosome 단위의 처리가 필요하다. 우리는 chromosome단위의 SNP data를 한 번에 처리가 가능한 시스템인 MarSel를 구현하였다

• The Korean Journal of Zoology
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• v.25 no.2
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• pp.81-92
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• 1982

G- and C-banding pattern analyses of striped field mice (Apodemus agrarius coreae) using 17 specimens from four localities in Korea revealed that centromeric heterochromatin results in the variation of No. 1 chromosome pair (telocentri $c_telocentric), i.e., centromeric heterochromatin sometimes appeared to be recognized as short arm. G- and C-banding patterns of four black rats (R. rattus rufescens) from two localities in Korea showed that No. 1 chromosome polymorphism (telocentri $c_telocentric) is due to pericentric inversion. In addition, G- and C-banding patterns of black rats mentioned above are idiogrammed.ammed.

• Proceedings of the Zoological Society Korea Conference
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• 2000.10a
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• pp.273.2-274
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• 2000

No Abstract, See Full Text

• Environmental Analysis Health and Toxicology
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• v.20 no.4 s.51
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• pp.303-309
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• 2005

Essential hypertension has been considered as multifactorial disease resulted from the interaction of both environmental and genetic factors. The renin-angiotensin system (RAS) plays an important role in the regulation of blood pressure homeostasis. Recently, a homologue of angiotensin I converting enzyme, ACE2 has been focused on as a candidate gene of essential hypertension in the experiments using animal model and human being. In this study, we carried out an association study in order to clarify the relationship between the A 1075G polymorphism in the ACE2 gene and essential hypertension in Korean subjects. Because this polymorphism is located on human chromosome X, the statistical analysis for each gender was performed separately. There were no significant differences in allele distribution of the A 1075G polymorphism in the ACE2 gene between normotensives and hypertensives in the both gender groups, respectively. However, this polymorphism was significantly associated with systolic blood pressure (SBP) and diastolic blood pressure (DBP) values in only female groups (P< 0.05). Thus, these results may suggest the probable role of ACE2 gene in the inter-individual susceptibility of female group to blood pressure variability.

• Journal of Genetic Medicine
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• v.3 no.1
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• pp.5-10
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• 1999

This is a case report of 46,XY female phenotype (46,XY karyotype, no pubic hair, blind vagina and absence of uterus)in an 18-year-old patient. To confirm whether a Y chromosome has a structural abnormality, fluorescent in situ hybridization (FISH) with the chromosome X/Y cocktail probe was simultaneously performed, and the six loci [PABY, RPS4Y(sy16, sy17), ZFY, DYS14] on the short arm, one locus (DYZ3) on the centromere and one locus (DYZ1) on the long arm were amplified by polymerase chain reaction (PCR). The probes used FISH hybridized to centromere of the X chromosome and heterochromatin region (Yq12) of the Y chromosome, and all PCR related Y chromosome showed positive band like normal male. From the results obtained, it seemed that the Y chromosome from the 46,XY female was structurely normal. Especially, the SRY gene has been equated with the mammalian testis-determining factor, and absence or point mutation in the SRY gene causes XY female. To detect the point mutations of SRY sequences, single-strand conformation polymorphism (SSCP) assay was used. Our results confirm that this patient has no mutation in the SRY gene on the Y chromosome.

• Asian Pacific Journal of Cancer Prevention
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• v.16 no.6
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• pp.2231-2235
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• 2015

Genome-wide association studies (GWASs) of the entire genome provide a systematic approach for revealing novel genetic susceptibility loci for breast cancer. However, genetic association studies have hitherto been primarily conducted in women of European ancestry. Therefofre we here performed a pilot GWAS with a single nucleotide polymorphism (SNP) array 5.0 platform from $Affymetrix^{(R)}$ that contains 443,813 SNPs to search for new genetic risk factors in 89 breast cancer cases and 46 healthy women of Indonesian ancestry. The case-control association of the GWAS finding set was evaluated using PLINK. The strengths of allelic and genotypic associations were assessed using logistic regression analysis and reported as odds ratios (ORs) and P values; P values less than $1.00{\times}10^{-8}$ and $5.00{\times}10^{-5}$ were required for significant association and suggestive association, respectively. After analyzing 292,887 SNPs, we recognized 11 chromosome loci that possessed suggestive associations with breast cancer risk. Of these, however, there were only four chromosome loci with identified genes: chromosome 2p.12 with the CTNNA2 gene [Odds ratio (OR)=1.20, 95% confidence interval (CI)=1.13-1.33, $P=1.08{\times}10^{-7}$]; chromosome 18p11.2 with the SOGA2 gene (OR=1.32, 95%CI=1.17-1.44, $P=6.88{\times}10^{-6}$); chromosome 5q14.1 with the SSBP2 gene (OR=1.22, 95%CI=1.11-1.34, $P=4.00{\times}10^{-5}$); and chromosome 9q31.1 with the TEX10 gene (OR=1.24, 95%CI=1.12-1.35, $P=4.68{\times}10^{-5}$). This study identified 11 chromosome loci which exhibited suggestive associations with the risk of breast cancer among Indonesian women.

• Asian Pacific Journal of Cancer Prevention
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• v.16 no.6
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• pp.2489-2493
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• 2015

Background: Loss of heterozygosity (LOH) on chromosomal regions is crucial in tumor progression and this study aimed to identify genome-wide LOH in pancreatic cancer. Materials and Methods: Single-nucleotide polymorphism (SNP) profiling data GSE32682 of human pancreatic samples snap-frozen during surgery were downloaded from Gene Expression Omnibus database. Genotype console software was used to perform data processing. Candidate genes with LOH were screened based on the genotype calls, SNP loci of LOH and dbSNP database. Gene annotation was performed to identify the functions of candidate genes using NCBI (the National Center for Biotechnology Information) database, followed by Gene Ontology, INTERPRO, PFAM and SMART annotation and UCSC Genome Browser track to the unannotated genes using DAVID (the Database for Annotation, Visualization and Integration Discovery). Results: The candidate genes with LOH identified in this study were MCU, MICU1 and OIT3 on chromosome 10. MCU was found to encode a calcium transporter and MICU1 could encode an essential regulator of mitochondrial $Ca^{2+}$ uptake. OIT3 possibly correlated with calcium binding revealed by the annotation analyses and was regulated by a large number of transcription factors including STAT, SOX9, CREB, NF-kB, PPARG and p53. Conclusions: Global genomic analysis of SNPs identified MICU1, MCU and OIT3 with LOH on chromosome 10, implying involvement of these genes in progression of pancreatic cancer.