• Communications for Statistical Applications and Methods
• /
• 제16권3호
• /
• pp.397-408
• /
• 2009

마이크로어레이 기술은 수만 개 유전자의 발현 패턴을 동시에 관찰하는 것을 가능하게 하였고, 이들을 하나씩 검정하여 찾아낸 특이발현 현상을 보이는 유전자를 중심으로 질병의 진단, 치료법 정립과 신약 개발을 위한 기본 정보를 확립하였다. 그러나 개별 유전자분석의 여러 문제점이 발견되면서 유전자들을 생물학적 대사경로나 염색체 위치가 같은 것끼리 묶은 집단을 분석하여 질병의 발생이나 생존에 영향을 미치는 집단을 찾는 방법이 제시되었다. 이러한 유전자 집단의 유의성에 대한 연구는 2002년에 MIT에서 비롯되어 GSEA, SAM-GS와 중심극한 정리의 개념을 이용한 모수적 방법인 PAGE 등이 사용되고 있다. 본 논문에서는 이들 통계량의 구조적 한계를 극복하고 계산이 간단한 새로운 모수적 방법을 제안하고 자료 분석을 통하여 효율성을 보였다.

• Genomics & Informatics
• /
• 제18권1호
• /
• pp.6.1-6.9
• /
• 2020

Acute leukemia represents the most common pediatric malignancy comprising diverse subtypes with varying prognosis and treatment outcomes. New and targeted treatment options are warranted for this disease. Patient-derived xenograft (PDX) models are increasingly being used for preclinical testing of novel treatment modalities. A novel approach involving targeted error-corrected RNA sequencing using ArcherDX HemeV2 kit was employed to compare 25 primary pediatric acute leukemia samples and their corresponding PDX samples. A comparison of the primary samples and PDX samples revealed a high concordance between single nucleotide variants and gene fusions whereas other complex structural variants were not as consistent. The presence of gene fusions representing the major driver mutations at similar allelic frequencies in PDX samples compared to primary samples and over multiple passages confirms the utility of PDX models for preclinical drug testing. Characterization and tracking of these novel cryptic fusions and exonal variants in PDX models is critical in assessing response to potential new therapies.

• 한국응용약물학회:학술대회논문집
• /
• 한국응용약물학회 1994년도 춘계학술대회 and 제3회 신약개발 연구발표회
• /
• pp.129-130
• /
• 1994

The science of toxicology is the understanding of the mechanisms by which exogenous agents produce deleterious effects in biological systems. The actions of chemicals such as drugs are ultimately exerted at the cellular and gene levels. Over the past decade. several in vitro alternative methods such as cultured cells for assessing the toxicity of various xenobiotics have been proposed to reduce the use of animals. In this workshop three advanced methods will be presented. These methods are novel important models for toxicologic studies. Dr. Tabuchis group has establishcd two immortalized gastric surface mucosa cell lines from the pminary cultore of gastric fundic mucosal cells of adult transgenic mice harboring a temperature sensitive simian virus 40 large T-anugen gene. As the immortalized cell lines of various tissues possess unique characteristics to maintain their normal functions for several months, these cell lines are extremely useful for not only toxicity testing but also pharmacological screening in new drug development. Professor Funatsu have studied the formation of spherical multicelluar aggregates of adult rat hepatocytes(spheroid) having tissue like structure. The sphcroid shown thre is a prototype module of an artificial liver support system. Thus, the urea synthesis activity of the artificial liver was maintained at least to days in 100％ rat blood plasma. Dr. Takezawa and his coworkers have developed a novel culture system of multicellular spheroids considered 〃organoids〃 by utilizing a thermo-responsive polymer as a substratum of anchorage dependent cells. His final goal is to reconstitute the organoids of various normal organs, e.g., liver, skin etc. and also abnormal deseased organs such as tumor.

• 종양간호연구
• /
• 제11권3호
• /
• pp.200-209
• /
• 2011

Purpose: The purpose of this micro-ethnography is to examine whether science and societal changes impact family communication patterns among a convenience sample of 16 Korean women. Methods: The authors observed family communication in the context of a new breast cancer genetic screening and diagnostic testing program to detect BRCA gene mutations in Korean women at highest risk. Results: Analysis of in-depth interviews and field notes taken during participant observation illustrated that communication patterns in families vary according to a woman's position in the family. If a grandmother tests positive for a gene mutation, her daughters make decisions on her behalf; they open and maintain the communication channel among family members. If a housewife is diagnosed with cancer and a genetic mutation, she immediately consults her husband and her sisters. The husband creates an open communication channel between his wife, his parents and his siblings. As a result, a woman's cancer is a concern for the whole family not merely a woman's secret or crisis. Conclusion: Cultural differences are important to consider when designing new genetic service programs in different countries.

• Genomics & Informatics
• /
• 제19권3호
• /
• pp.34.1-34.6
• /
• 2021

Digital PCR (dPCR) is the third-generation PCR that enables real-time absolute quantification without reference materials. Recently, global diagnosis companies have developed new dPCR equipment. In line with the development, the Lab On An Array (LOAA) dPCR analyzer (Optolane) was launched last year. The LOAA dPCR is a semiconductor chip-based separation PCR type equipment. The LOAA dPCR includes Micro Electro Mechanical System that can be injected by partitioning the target gene into 56 to 20,000 wells. The amount of target gene per wells is digitized to 0 or 1 as the number of well gradually increases to 20,000 wells because its principle follows Poisson distribution, which allows the LOAA dPCR to perform precise absolute quantification. LOAA determined region of interest first prior to dPCR operation. To exclude invalid wells for the quantification, the LOAA dPCR has applied various filtering methods using brightness, slope, baseline, and noise filters. As the coronavirus disease 2019 has now spread around the world, needs for diagnostic equipment of point of care testing (POCT) are increasing. The LOAA dPCR is expected to be suitable for POCT diagnosis due to its compact size and high accuracy. Here, we describe the quantitative principle of the LOAA dPCR and suggest that it can be applied to various fields.

• 생명과학회지
• /
• 제15권1호
• /
• pp.45-48
• /
• 2005

서울대공원에서 사육중인 Miniature horse 10두의 혈통정립을 목적으로 PCR에 의한 성별 판정 및 16개 microsatellite marker를 사용하여 친자감정을 실시하였다. 성별 판정에서 430 bp의 SRY band가 관찰된 7두는 숫말로 판정되었고, 친자감정에서는 멘델의 유전양식에 부합된 3두가 친자관계가 확인되었다. 향후 Miniature horse의 혈통보존 및 관리에 유용한 자료가 될 것으로 사료된다.

• Journal of Pharmaceutical Investigation
• /
• 제34권6호
• /
• pp.465-469
• /
• 2004

Colloidal gold nanoparticles might be of use as nano scale delivery systems of various therapeutic materials in the future. Recent studies have reported the feasibility of colloidal gold nanoparticles as gene delivery systems or protein delivery systems. In this study, we aimed to develop a short-step method useful for screening the optimal coating conditions of colloidal gold nanoparticles with proteins. We observed that colloidal gold nanoparticles have properties of changing its unique color when they were exposed to NaCl solution. Taking advantage of the color changing properties of colloidal gold nanoparticles, we applied the color testing method of colloidal gold nanoparticles solutions for evaluating the protein coating nature. Using bovine serum albumin as a model protein, we tested the protein coating of colloidal gold nanoparticles via the color change upon NaCl addition. The optimal coating concentration and coating conditions of colloidal gold nanoparticles with bovine serum albumin were fixed using the color testing methods. We suggest that the color testing method might be applied to optimize the coating condition of colloidal gold nanoparticles with other therapeutic proteins.

• Childhood Kidney Diseases
• /
• 제28권1호
• /
• pp.8-15
• /
• 2024

With the rapid evolution of diagnostic tools, particularly next-generation sequencing, the identification of genetic diseases, predominantly those with pediatric-onset, has significantly advanced. However, this progress presents challenges that span from selecting appropriate tests to the final interpretation of results. This review examines various genetic testing methodologies, each with specific indications and characteristics, emphasizing the importance of selecting the appropriate genetic test in clinical practice, taking into account factors like detection range, cost, turnaround time, and specificity of the clinical diagnosis. Interpretation of variants has become more challenging, often requiring further validation and significant resource allocation. Laboratories primarily classify variants based on the American College of Medical Genetics and Genomics and the Association for Clinical Genomic Science guidelines, however, this process has limitations. This review underscores the critical role of clinicians in matching patient phenotypes with reported genes/variants and considering additional factors such as variable expressivity, disease pleiotropy, and incomplete penetrance. These considerations should be aligned with specific gene-disease characteristics and segregation results based on an extended pedigree. In conclusion, this review aims to enhance understanding of the complexities of clinical genetic testing, advocating for a multidisciplinary approach to ensure accurate diagnosis and effective management of rare genetic diseases.

• Asian Pacific Journal of Cancer Prevention
• /
• 제13권11호
• /
• pp.5477-5482
• /
• 2012

Background: The HER-2/neu gene is altered in 15-20% of breast cancer patients. Immunohistochemistry (IHC) is considered to be the most cost-effective method for HER-2 detection in many countries. Approximately 8,000 new cases of breast cancer are observed annually in Iran. The aims of this study were to conduct a systematic review of the literature on the rate of HER-2-positive breast cancer diagnosed by IHC in Iran. Methods: A systematic search of the medical literature using the Medline/PubMed, ISI and SID databases revealed articles published in the English and Persian languages evaluating HER-2-positive breast cancer in Iran. Results: From 22 studies, 3,033 patients were evaluated, of whom 1,350 were diagnosed as HER-2-positive by IHC HER-2 testing. The mean percentage of HER-2-positive patients was 44.5%, which is higher than that recorded in international statistics. Results of this meta-analysis showed a significant heterogeneity between ratios. There was a statistically significant difference between the results of pre- and post implementation of 2007 American Society of Clinical Oncology/College of American Pathologists (ASCO/CAP) guideline. IHC HER-2 testing has been performed in Iran for over 10 years. Similar to many other countries, before establishment of an infrastructure for IHC diagnostic tests, HER-2 testing was routinely performed in Iran. Our study showed that the statistics reported from Iran varied widely; for instance, the rate of HER-2-positive cases varied from 23.3% to 81.0%. Conclusions: Our results demonstrate that the lack of standardization and harmonization of this test have led to marked variations in breast cancer diagnosis in Iran.

• Computers and Concrete
• /
• 제27권4호
• /
• pp.319-332
• /
• 2021

The performance of gene expression programming (GEP) in predicting the compressive strength of bacteria-incorporated geopolymer concrete (GPC) was examined in this study. Ground-granulated blast-furnace slag (GGBS), new bacterial strains, fly ash (FA), silica fume (SF), metakaolin (MK), and manufactured sand were used as ingredients in the concrete mixture. For the geopolymer preparation, an 8 M sodium hydroxide (NaOH) solution was used, and the ambient curing temperature (28℃) was maintained for all mixtures. The ratio of sodium silicate (Na2SiO3) to NaOH was 2.33, and the ratio of alkaline liquid to binder was 0.35. Based on experimental data collected from the literature, an evolutionary-based algorithm (GEP) was proposed to develop new predictive models for estimating the compressive strength of GPC containing bacteria. Data were classified into training and testing sets to obtain a closed-form solution using GEP. Independent variables for the model were the constituent materials of GPC, such as FA, MK, SF, and Bacillus bacteria. A total of six GEP formulations were developed for predicting the compressive strength of bacteria-incorporated GPC obtained at 1, 3, 7, 28, 56, and 90 days of curing. 80% and 20% of the data were used for training and testing the models, respectively. R2 values in the range of 0.9747 and 0.9950 (including train and test dataset) were obtained for the concrete samples, which showed that GEP can be used to predict the compressive strength of GPC containing bacteria with minimal error. Moreover, the GEP models were in good agreement with the experimental datasets and were robust and reliable. The models developed could serve as a tool for concrete constructors using geopolymers within the framework of this research.