• Asian Pacific Journal of Cancer Prevention
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• v.16 no.16
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• pp.7343-7350
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• 2015

Genetic changes associated with acute lymphoblastic leukemia (ALL) provide very important diagnostic and prognostic information with a direct impact on patient management. Detection of chromosome abnormalities by conventional cytogenetics combined with fluorescence in situ hybridization (FISH) play a very significant role in assessing risk stratification. Identification of specific chromosome abnormalities has led to the recognition of genetic subgroups based on reciprocal translocations, deletions and modal number in B or T-cell ALL. In the last twelve years 102 newly diagnosed childhood/adult ALL bone marrow samples were analysed for chromosomal abnormalities with conventional G-banding, and FISH (selected cases) using specific probes in our hospital. G-banded karyotype analysis found clonal numerical and/or structural chromosomal aberrations in 74.2% of cases. Patients with pseudodiploidy represented the most frequent group (38.7%) followed by high hyperdiploidy group (12.9%), low hyperdiploidy group (9.7%), hypodiploidy (<46) group (9.7%) and high hypertriploidy group (3.2%). The highest observed numerical chromosomal alteration was high hyperdiploidy (12.9%) with abnormal karyotypes while abnormal 12p (7.5%) was the highest observed structural abnormality followed by t(12;21)(p13.3;q22) resulting in ETV6/RUNX1 fusion (5.4%) and t(9;22)(q34.1;q11.2) resulting in BCR/ABL1 fusion (4.3%). Interestingly, we identified 16 cases with rare and complex structural aberrations. Application of the FISH technique produced major improvements in the sensitivity and accuracy of cytogenetic analysis with ALL patients. In conclusion it confirmed heterogeneity of ALL by identifying various recurrent chromosomal aberrations along with non-specific rearrangements and their association with specific immunophenotypes. This study pool is representative of paediatric/adult ALL patients in Oman.

• Asian Pacific Journal of Cancer Prevention
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• v.16 no.7
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• pp.2713-2717
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• 2015

Background: Possible associations between the single nucleotide polymorphism (SNP) rs8034191 in the aminoglycosidephosphotransferase domain containing 1 (AGPHD1) gene and lung cancer risk have been studied by many researchers but the results have been contradictory. Materials and Methods: A computerized search for publications on rs8034191 and lung cancer risk was performed. Odds ratios (ORs) with 95% confidence intervals (CIs) were calculated to assess the association between rs8034191 and lung cancer risk with 13 selected case-control studies. Sensitivity analysis, test of heterogeneity, cumulative meta-analysis, and assessment of bias were also performed. Results: A significant association between rs8034191 and lung cancer susceptibility was found using the dominant genetic model (OR=1.344, 95% CI: 1.285-1.406), the additive genetic model (OR=1.613, 95% CI: 1.503-1.730), and the recessive genetic model (OR=1.408, 95% CI: 1.319-1.503). Moreover, an increased lung cancer risk was found with all genetic models after stratification of ethnicity. Conclusions: The association between rs8034191 and lung cancer risk was significant using multiple genetic models, suggesting that rs8034191 is a risk factor for lung cancer. Further functional studies of this polymorphism and lung cancer risk are warranted.

• Journal of Korean Society of Forest Science
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• v.88 no.3
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• pp.408-418
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• 1999

On the basin of RAPD analysis, genetic diversity and structure of the natural populations of Abies holophylla was estimated by AMOVA procedure. The average value of percent of polymorphic markers was 71.9%. Most variation existed among individuals within population(80.2%). Genetic differentiation among populations(${\Phi}_{ST}$) was 0.198. When the populations were grouped as two region(i.e., Taebaek and Sobaek Mountain Regions), 8.5% of the total genetic variation was explained as regional differences. The heterogeneity of molecular variance among populations was investigated with Bartlett's test, which revealed that populations of Mt. Taebaek and Mt. Gariwang were more heterogeneous. Generally, the populations of Taebaek Mountain Reion were more heterogeneous than those of Sobaek Mountain Reion. Finally, the applicability of AMOVA to the populations frenetic study was discussed in comparison with other measures of genetic differentiation which were widely used.

• The Plant Pathology Journal
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• v.35 no.1
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• pp.41-50
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• 2019

Sugarcane bacilliform viruses (SCBV), which belong to the genus Badnavirus, family Caulimoviridae, are an important DNA virus complex that infects sugarcane. To explore the genetic diversity of the sugarcane-infecting badnavirus complex in China, we tested 392 sugarcane leaf samples collected from Fujian, Yunnan, and Hainan provinces for the occurrence of SCBV by polymerase chain reaction (PCR) assays using published primers SCBV-F and SCBV-R that target the reverse transcriptase/ribonuclease H (RT/RNase H) regions of the viral genome. A total of 111 PCR-amplified fragments (726 bp) from 63 SCBV-positive samples were cloned and sequenced. A neighbor-joining phylogenetic tree was constructed based on the SCBV sequences from this study and 34 published sequences representing 18 different phylogroups or genotypes (SCBV-A to -R). All SCBV-tested isolates could be classified into 20 SCBV phylogenetic groups from SCBV-A to -T. Of nine SCBV phylogroups reported in this study, two novel phylogroups, SCBV-S and SCBV-T, that share 90.0-93.2% sequence identity and show 0.07-0.11 genetic distance with each other in the RT/RNase H region, are proposed. SCBV-S had 57.6-92.2% sequence identity and 0.09-0.66 genetic distance, while SCBV-T had 58.4-90.0% sequence identity and 0.11-0.63 genetic distance compared with the published SCBV phylogroups. Additionally, two other Badnavirus species, Sugarcane bacilliform MO virus (SCBMOV) and Sugarcane bacilliform IM virus (SCBIMV), which originally clustered in phylogenetic groups SCBV-E and SCBV-F, respectively, are first reported in China. Our findings will help to understand the level of genetic heterogeneity present in the complex of Badnavirus species that infect sugarcane.

• Asian Pacific Journal of Cancer Prevention
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• v.15 no.15
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• pp.6071-6074
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• 2014

Background: Evidence suggests that the rs11615 (C>T) polymorphism in the ERCC1 gene may be a risk factor for gynecological tumors. However, results have not been consistent. Therefore we performed this meta-analysis. Methods: Eligible studies were identified by search of PubMed, MEDLINE and Chinese National Knowledge Infrastructure (CNKI). Odds ratios (ORs) and 95% confidence intervals (CIs) were applied to assess associations between rs11615 (C>T) and gynecological tumor risk. Heterogeneity among studies was tested and sensitivity analysis was applied. Results: A total of 6 studies were identified, with 1,766 cases and 2,073 controls. No significant association was found overall between rs11615 (C>T) polymorphism and gynecological tumors susceptibility in any genetic model. In further analysis stratified by cancer type, significantly elevated ovarian cancer risk was observed in the homozygote and recessive model comparison (TT vs. CC: OR=1.69, 95% CI=1.03-2.77, heterogeneity=0.876; TT vs. CT/CC: OR=1.72, 95% CI=1.07-2.77, heterogeneity=0.995). Conclusion: The results of the present meta-analysis suggest that there is no significant association between the rs11615 (C>T) polymorphism and gynecological tumor risk, but it had a increased risk in ovarian cancer.

• Journal of Korean Society of Forest Science
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• v.90 no.1
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• pp.43-54
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• 2001

Genetic differentiation of populations is resulted from the environmental and the genetic effects, and the interactions between them. Whereas, the major factors influencing to the genetic differentiation within populations are the gene flow induced by seed or pollen dispersial, the microsite heterogeneity, and the density-dependent distribution of individuals. For the purpose of studying spatial genetic structure and the distribution pattern of Korean pines(Pinus koraiensis), we set up one $100{\times}100m$ plot at a Korean pine stand in Quercus mongolica community on Mt. Jumbong in Korea. To estimate the coefficient of spatial autocorrelation as Moran's index and an analogue, simple block distance, isozyme markers were analyzed in 325 Korean pines. For 11 polymorphic loci observed in 9 enzyme systems, the average percentage of polymorphic loci, the observed and expected heterozygocity were 72.2% 0.200, and 0.251, respectively. It was revealed the excess of homozygotes was observed in the plot, which suggests that here may be more number of consanguineous trees than expected. On the basis of isozyme genotypes observed in this study, 325 trees were classified into 147 groups in which the maximum number of trees for one group was 34. From the distance class of 24-32m, the genetic heterogeneity began to increase. The variation of simple block distance against the growth performance by tree height and diameter also showed the same trend at 24~32m class. According to high fixation index(F=0.204), the spatial genetic structure within a stand, the analysis of the growth performance, and the distribution patterns of identical genotypes, we inferred that the genetic structure of a Korean pine stand in Mt. Jumbong has been maintained rather density-dependent mechanism than the gene flow, such as the pollen dispersial or the heavy input of seeds following the forest gaps. The genetic patchy size was determined between 24~32m, which suggests that the selection of individuals for the ex situ conservation of Korean pine in Mt. Jumbong may be desirable to be made with the spatial distance over 37 meters between trees.

• The KIPS Transactions:PartD
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• v.18D no.2
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• pp.89-100
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• 2011

The CNV (Copy Number Variation) which is one of the genetic structural variations in human genome is closely related with the function of gene. In particular, the genome-wide association studies for genetic diseased persons have been researched. However, there have been few studies which infer the genetic function of CNV with normal human. In this paper, we propose the analysis method to reveal the functional relationship between common CNV and genes without considering their genomic loci. To achieve that, we propose the data integration method for heterogeneity biological data and novel measurement which can calculate the correlation between common CNV and genes. To verify the significance of proposed method, we has experimented several verification tests with GO database. The result showed that the novel measurement had enough significance compared with random test and the proposed method could systematically produce the candidates of genetic function which have strong correlation with common CNV.

• Biomolecules & Therapeutics
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• v.24 no.3
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• pp.207-243
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• 2016

Autism spectrum disorder (ASD) is a neurodevelopmental disorder characterized by social and communication impairments, as well as repetitive and restrictive behaviors. The phenotypic heterogeneity of ASD has made it overwhelmingly difficult to determine the exact etiology and pathophysiology underlying the core symptoms, which are often accompanied by comorbidities such as hyperactivity, seizures, and sensorimotor abnormalities. To our benefit, the advent of animal models has allowed us to assess and test diverse risk factors of ASD, both genetic and environmental, and measure their contribution to the manifestation of autistic symptoms. At a broader scale, rodent models have helped consolidate molecular pathways and unify the neurophysiological mechanisms underlying each one of the various etiologies. This approach will potentially enable the stratification of ASD into clinical, molecular, and neurophenotypic subgroups, further proving their translational utility. It is henceforth paramount to establish a common ground of mechanistic theories from complementing results in preclinical research. In this review, we cluster the ASD animal models into lesion and genetic models and further classify them based on the corresponding environmental, epigenetic and genetic factors. Finally, we summarize the symptoms and neuropathological highlights for each model and make critical comparisons that elucidate their clinical and neurobiological relevance.

• Parasites, Hosts and Diseases
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• v.55 no.2
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• pp.159-165
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• 2017

Vivax malaria reemerged in Korea in 1993 and the outbreak has been continued with fluctuating numbers of annual indigenous cases. Understanding the nature of the genetic population of Plasmodium vivax circulating in Korea is beneficial for the knowledge of the nationwide parasite heterogeneity and in the implementation of malaria control programs in the country. Previously, we analyzed polymorphic nature of merozoite surface protein-1 (MSP-1) and MSP-$3{\alpha}$ in Korean P. vivax population and identified the Korean P. vivax population has been diversifying rapidly, with the appearance of parasites with new genetic subtypes, despite the recent reduction of the disease incidence. In the present study, we developed simple PCR-RFLP methods for rapid subtyping of MSP-1 and MSP-$3{\alpha}$ of Korean P. vivax isolates. These PCR-RFLP methods were able to easily distinguish each subtype of Korean P. vivax MSP-1 and MSP-$3{\alpha}$ with high accuracy. The PCR-RFLP subtyping methods developed here would be easily applied to massive epidemiological studies for molecular surveillance to understand genetic population of P. vivax and to supervise the genetic variation of the parasite circulating in Korea.

• Journal of Genetic Medicine
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• v.13 no.1
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• pp.20-25
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• 2016

Purpose: Xeroderma pigmentosum (XP) is rare autosomal recessive genetic disorder of DNA repair in which the ability to repair damage caused by ultraviolet light is deficient. We reported the first molecularly confirmed Korean patient of XP by targeted exome sequencing. The prevalence of XP included all subtype and carrier frequency of XP-A the using public data were estimated for the first time in South Korea. Materials and Methods: We described a 4-year-old Korean girl with clinical diagnosis of XP. We performed targeted exome sequencing in the patient for genetic confirmation considering disease genetic heterogeneity and for differential diagnosis. We verified a carrier frequency of c.390-1G>C in XPA gene known as mutational hot spot using Korean Reference Genome Data Base. We estimated the period prevalence of all subtypes of XP based on claims data of the Health Insurance Review and Assessment Service in South Korea. Results: We identified homozygous splicing mutation of XPA (c.390-1G>C) in the patient. The carrier frequency of risk for XPA (c.390-1G>C) was relatively high 1.608 e-03 (allele count 2/1244). The prevalence of XP in South Korea was 0.3 per million people. Conclusion: We expect that c.390-1G>C is hot spot for the mutation of XPA and possible founder variant in South Korea. However, the prevalence in South Korea was extremely low compared with Western countries and Japan.