• Genomics & Informatics
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• 제14권4호
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• pp.138-148
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• 2016

The success of genome-wide association studies (GWASs) has enabled us to improve risk assessment and provide novel genetic variants for diagnosis, prevention, and treatment. However, most variants discovered by GWASs have been reported to have very small effect sizes on complex human diseases, which has been a big hurdle in building risk prediction models. Recently, many statistical approaches based on penalized regression have been developed to solve the "large p and small n" problem. In this report, we evaluated the performance of several statistical methods for predicting a binary trait: stepwise logistic regression (SLR), least absolute shrinkage and selection operator (LASSO), and Elastic-Net (EN). We first built a prediction model by combining variable selection and prediction methods for type 2 diabetes using Affymetrix Genome-Wide Human SNP Array 5.0 from the Korean Association Resource project. We assessed the risk prediction performance using area under the receiver operating characteristic curve (AUC) for the internal and external validation datasets. In the internal validation, SLR-LASSO and SLR-EN tended to yield more accurate predictions than other combinations. During the external validation, the SLR-SLR and SLR-EN combinations achieved the highest AUC of 0.726. We propose these combinations as a potentially powerful risk prediction model for type 2 diabetes.

• Interdisciplinary Bio Central
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• 제4권4호
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• pp.11.1-11.8
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• 2012

Genes that are indispensable for survival are referred to as essential gene. Due to the momentous significance of these genes for cellular activity they can be selected potentially as drug targets. Here in this study, an essential gene for Streptococcus suis was predicted using coherent statistical analysis and powerful genome comparison computational method. At first the whole genome protein scatter plot was generated and subsequently, on the basis of statistical significance, a reference genome was chosen. The parameters set forth for selecting the reference genome was that the genome of the query (Streptococcus suis) and subject must fall in the same genus and yet they must vary to a good degree. Streptococcus pneumoniae was found to be suitable as the reference genome. A whole genome comparison was performed for the reference (Streptococcus pneumoniae) and the query genome (Streptococcus suis) and 14 conserved proteins from them were subjected to a screen for potential essential gene property. Among those 14 only one essential gene was found to be with impressive similarity score between reference and query. The essential gene encodes for a type of 'Clp protease'. Clp proteases play major roles in degrading misfolded proteins. Results found here should help formulating a drug against Strptococcus suis which is responsible for mild to severe clinical conditions in human. However, like many other computational studies, the study has to be validated furthermore through in vitro assays for concrete proof.

• 종양간호연구
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• 제12권4호
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• pp.267-273
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• 2012

Purpose: The purpose of this review article is to introduce how the Korean Society of Genetic Nursing (KSGN) has evolved and tried to translate genomic knowledge to nursing practice, and then to suggest the future role of genetic nurses in Korea. Methods: A literature review was performed and the current status of genetic counselling in Korea was explored. Then the educational and clinical experiences of the authors were incorporated. Finally, the main activities of Korean nursing for genetics were identified. Results: Two types of genetic counsellor certification have been issued in Korea: one is issued by the Korean Society of Genetic Medicine, another by the Korean Society of Breast Cancer since June 2011. A few Korean nursing researchers have continuously performed research related to genetic nursing and undertook several research projects funded by the government since 2003. In February 2011, KSGN was established and is now trying to establish further international networks. Conclusion: Nursing genetic experts should be trained to integrate all specialties for genetic counselling, so they can provide holistic genetic services including ethical, legal, and social issues (ELSI).

• Clinical and Experimental Reproductive Medicine
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• 제42권3호
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• pp.77-85
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• 2015

One of the key factors of early development is the specification of competence between the oocyte and the sperm, which occurs during gametogenesis. However, the starting point, growth, and maturation for acquiring competence during spermatogenesis and oogenesis in mammals are very different. Spermatogenesis includes spermiogenesis, but such a metamorphosis is not observed during oogenesis. Glycosylation, a ubiquitous modification, is a preliminary requisite for distribution of the structural and functional components of spermatids for metamorphosis. In addition, glycosylation using epididymal or female genital secretory glycans is an important process for the sperm maturation, the acquisition of the potential for fertilization, and the acceleration of early embryo development. However, nonemzymatic unexpected covalent bonding of a carbohydrate and malglycosylation can result in falling fertility rates as shown in the diabetic male. So far, glycosylation during spermatogenesis and the dynamics of the plasma membrane in the process of capacitation and fertilization have been evaluated, and a powerful role of glycosylation in spermatogenesis and early development is also suggested by structural bioinformatics, functional genomics, and functional proteomics. Further understanding of glycosylation is needed to provide a better understanding of fertilization and embryo development and for the development of new diagnostic and therapeutic tools for infertility.

• Genomics & Informatics
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• 제5권2호
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• pp.83-87
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• 2007

The analysis of DNA microarray data is a rapidly evolving area of bioinformatics, and various types of microarray are emerging as some of the most exciting technologies for use in biological and clinical research. In recent years, microarray technology has been utilized in various applications such as the profiling of mRNAs, assessment of DNA copy number, genotyping, and detection of methylated sequences. However, the analysis of these heterogeneous microarray platform experiments does not need to be performed separately. Rather, these platforms can be co-analyzed in combination, for cross-validation. There are a number of separate laboratory information management systems (LIMS) that individually address some of the needs for each platform. However, to our knowledge there are no unified LIMS systems capable of organizing all of the information regarding multi-platform microarray experiments, while additionally integrating this information with tools to perform the analysis. In order to address these requirements, we developed a web-based LIMS system that provides an integrated framework for storing and analyzing microarray information generated by the various platforms. This system enables an easy integration of modules that transform, analyze and/or visualize multi-platform microarray data.

• Genomics & Informatics
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• 제16권2호
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• pp.30-35
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• 2018

Patient-derived xenograft (PDX) models are useful tools for tumor biology research and testing the efficacy of candidate anticancer drugs targeting the druggable mutations identified in tumor tissue. However, it is still unknown how much of the genetic alterations identified in primary tumors are consistently detected in tumor tissues in the PDX model. In this study, we analyzed the genetic alterations of three primary colorectal cancers (CRCs) and matched xenograft tissues in PDX models using a next-generation sequencing cancer panel. Of the 17 somatic mutations identified from the three CRCs, 14 (82.4%) were consistently identified in both primary and xenograft tumors. The other three mutations identified in the primary tumor were not detected in the xenograft tumor tissue. There was no newly identified mutation in the xenograft tumor tissues. In addition to the somatic mutations, the copy number alteration profiles were also largely consistent between the primary tumor and xenograft tissue. All of these data suggest that the PDX tumor model preserves the majority of the key mutations detected in the primary tumor site. This study provides evidence that the PDX model is useful for testing targeted therapies in the clinical field and research on precision medicine.

• Journal of Genetic Medicine
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• 제11권1호
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• pp.31-35
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• 2014

Bardet-Biedl syndrome (BBS) is a rare ciliopathy generally inherited with an autosomal recessive pattern. BBS is characterized by 6 primary features namely retinal dystrophy, obesity, postaxial polydactyly, renal dysfunction, learning difficulties, and hypogonadism and a wide range of secondary features. To date, mutations in 16 genes have been identified as causative factors for BBS. Among them, the BBS1 and BBS10 genes are major disease-causing genes, and each of these gene mutations presents in more than 20% of all BBS patients. Genotype-phenotype correlations have not been observed in BBS, and there can be phenotypic overlap between BBS and other ciliopathies. In Korea, no molecular, genetically confirmed case of BBS has been reported to date. Herein, we describe the case of the first Korean siblings with BBS resulting from 2 BBS10 gene mutations who showed typical clinical phenotypes, including retinal dystrophy, obesity, intellectual disability, cystic tubular disease, and postaxial polydactyly.

• Journal of Genetic Medicine
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• 제11권1호
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• pp.27-30
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• 2014

Brachydactyly type C is a limb malformation characterized by shortening of the second, third, and fifth middle and/or proximal phalanges, but it has variable phenotypic expressivity. Mutations in the growth differentiation factor-5 (GDF5) gene cause isolated brachydactyly C. Herein, we report a familial case with isolated brachydactyly type C characterized by brachymesophalangy of both second and third digits, with a GDF5 missense mutation, and discuss the phenotypic variability of the condition. Identifying more cases with genetic confirmation will help elucidate the clinical and genetic characteristics of this condition in the Korean population.

• Journal of Genetic Medicine
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• 제6권1호
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• pp.8-24
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• 2009

난청의 약 50%는 유전적 요소가 원인이기 때문에 난청의 유전적 배경을 이해하는 것은 중요하다. 현재까지 150개 이상의 원인유전자들이 밝혀져 있다. 이번 종설에서는 유전성 난청의 분류, 유전성 난청 원인규명의 난점, 유전성 난청과 관련된 내이의 구조와 기능, 증후군성난청, 비증후군성난청, 미토콘드리아 유전성 난청, 그리고 다인자성 난청에 관해 논하고자 한다. 그리고 유전성 난청을 가진 환자의 치료적 접근과 유전적 상담을 간략하게 설명하고, 마지막으로 유전성 난청에 대한 앞으로의 연구 방향을 제시하고자 한다.

• Journal of Genetic Medicine
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• 제10권1호
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• pp.1-6
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• 2013

Chronic granulomatous disease (CGD) is a rare inherited disorder of a defective NADPH oxidase enzyme, resulting in very low or no production of superoxide and subsequent reactive oxygen species. Consequently, patients with CGD are highly susceptible to severe bacterial and fungal infections. CGD is a genetically heterogeneous disease caused by defects in any one of the genes encoding the NADPH oxidase components. CGD generally affects about 3-4 per 1,000,000 individuals; thus, it is surprising that the prevalence of CGD on Jeju Island is 34.3 per 1,000,000 individuals. At present, 20 patients with CGD from 14 unrelated families on Jeju Island have been identified; nine males and 11 females. All patients with CGD tested on Jeju Island had an identical and homozygous mutation (c.7C>T in CYBA, p.Q3X in $p22^{phox}$). Therefore, all patients were autosomal recessive form of CGD. This strongly suggests that the unique and identical mutation in CYBA may be inherited from a common proband. Using mutation-specific primers to detect the mutated allele in CYBA, the frequency of subjects carrying a mutated allele was 1.3% of enrolled subjects from Seogwipo City. Further studies are necessary to elucidate how frequently this mutant allele occurs in the population on Jeju Island. Additionally, it is important to construct a national registry system to understand the pathophysiology of CGD and develop a strategy for long-term therapy.