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Integrated genome sizing (IGS) approach for the parallelization of whole genome analysis
Sona, Peter,Hong, Jong Hui,Lee, Sunho,Kim, Byong Joon,Hong, Woon-Young,Jung, Jongcheol,Kim, Han-Na,Kim, Hyung-Lae,Christopher, David,Herviou, Laurent,Im, Young Hwan,Lee, Kwee-Yum,Kim, Tae Soon,Jung, J BioMed Central 2018 BMC bioinformatics Vol.19 No.1
<P><B>Background</B></P><P>The use of whole genome sequence has increased recently with rapid progression of next-generation sequencing (NGS) technologies. However, storing raw sequence reads to perform large-scale genome analysis pose hardware challenges. Despite advancement in genome analytic platforms, efficient approaches remain relevant especially as applied to the human genome. In this study, an Integrated Genome Sizing (IGS) approach is adopted to speed up multiple whole genome analysis in high-performance computing (HPC) environment. The approach splits a genome (GRCh37) into 630 chunks (fragments) wherein multiple chunks can simultaneously be parallelized for sequence analyses across cohorts.</P><P><B>Results</B></P><P>IGS was integrated on Maha-Fs (HPC) system, to provide the parallelization required to analyze 2504 whole genomes. Using a single reference pilot genome, NA12878, we compared the NGS process time between Maha-Fs (NFS SATA hard disk drive) and SGI-UV300 (solid state drive memory). It was observed that SGI-UV300 was faster, having 32.5 mins of process time, while that of the Maha-Fs was 55.2 mins.</P><P><B>Conclusions</B></P><P>The implementation of IGS can leverage the ability of HPC systems to analyze multiple genomes simultaneously. We believe this approach will accelerate research advancement in personalized genomic medicine. Our method is comparable to the fastest methods for sequence alignment.</P><P><B>Electronic supplementary material</B></P><P>The online version of this article (10.1186/s12859-018-2499-1) contains supplementary material, which is available to authorized users.</P>
Genotoxicity Studies on Carrageenan : Short-term In Vitro Assays
Young-Shin Chung,Ki-Hwan Eum,Seon-A Choi,Se-Wook Oh,Sue Nie Park,Young-Na Yum,Joo-Hwan Kim,Young-Rok Seo,Michael Lee 한국독성학회 2009 Toxicological Research Vol.25 No.1
Carrageenan is a naturally-occurring sulfated polygalactan which has been widely used in the dairy industry and a gelling agent in non-dairy products. In this study, four short-term in vitro genotoxicity assays were investigated to evaluate the potential genotoxic effects of carrageenan. The mutagenicity of carrageenan was evaluated up to a maximum dose of 5 ㎎/plate in Ames test. There was no increase in the number of revertant colonies compared to its negative control at any dose in all of strains tested. To assess clastogenic effect, the in vitro chromosomal aberration assay was performed using Chinese hamster lung cells. Carrageenan was not considered to be clastogenic in this assay at up to the highest feasible concentration which could be evaluated. The in vitro comet assay and micronucleus test results obtained on L5178Y cells also revealed that carrageenan has no genotoxicity potential, although there was a marginal increase in micronuclei frequencies and DNA damage in the respective micronucleus and comet assays. Taken together, our results indicate that carrageenan was not genotoxic based on four in vitro genotoxicity results.
OECD 급성경구투여독성시험 지침의 국내 확립 및 검증
조영래 ( Young Rae Cho ),염영나 ( Young Na Yum ),한의식 ( Eui Sik Han ),곽승준 ( Seung Jun Kwack ),김형섭 ( Hyung Sub Kim ),강미선 ( Mi Sun Kang ),이진영 ( Jin Young Lee ),오재호 ( Jae Ho Oh ),임채형 ( Chae Hyung Lim ),김대성 ( Da 한국동물실험대체법학회 2008 동물실험대체법학회지 Vol.2 No.2
As the study about the non-animal tests came to be internationally active and the interest in the animal welfare gradually became increased, OECD TG (Test Guideline) 401 that has been used since 1987 was abolished in 2002. Because TG401 is acute oral toxicity method depending on survival and death of many animals, it was heavily criticized. Therefore, the three alternative methods were developed. OECD TG420 and TG423 determine the class of chemicals according to GHS (Globally Harmonized Classification System for Chemical Substances and Mixtures) classification and OECD TG425 suggests the predicted LD50 of chemicals using AOT425 program. In this study, 10 chemicals were selected. The internationally admitted TG420, TG423 and TG425 were introduced and established through the method that these chemicals were orally administrated to SD female rats and then, the results were observed. Each chemical belonged to already known GHS class in the study using TG420 and TG423 and predicted LD50 was same or higher in the study using TG425 compared to already known LD50 value. In conclusion, the result of our study confirmed the decrease in the animal number and validated. The international harmonization of the non-animal tests will be pursued through this validation study.
Genotoxicity Studies on Carrageenan: Short-term In Vitro Assays
Chung, Young-Shin,Eum, Ki-Hwan,Choi, Seon-A,Oh, Se-Wook,Park, Sue-Nie,Yum, Young-Na,Kim, Joo-Hwan,Seo, Young-Rok,Lee, Michael Korean Society of ToxicologyKorea Environmental Mu 2009 Toxicological Research Vol.26 No.1
Carrageenan is a naturally-occurring sulfated polygalactan which has been widely used in the dairy industry and a gelling agent in non-dairy products. In this study, four short-term in vitro genotoxicity assays were investigated to evaluate the potential genotoxic effects of carrageenan. The mutagenicity of carrageenan was evaluated up to a maximum dose of 5 mg/plate in Ames test. There was no increase in the number of revertant colonies compared to its negative control at any dose in all of strains tested. To assess clastogenic effect, the in vitro chromosomal aberration assay was performed using Chinese hamster lung cells. Carrageenan was not considered to be clastogenic in this assay at up to the highest feasible concentration which could be evaluated. The in vitro comet assay and micronucleus test results obtained on L5178Y cells also revealed that carrageenan has no genotoxicity potential, although there was a marginal increase in micronuclei frequencies and DNA damage in the respective micronucleus and comet assays. Taken together, our results indicate that carrageenan was not genotoxic based on four in vitro genotoxicity results.
연구논문 : 말초혈액을 이용한 초고속 유전독성평가법 개발 연구
안일영 ( Il Young Ahn ),김주환 ( Ju Hwan Kim ),임대현 ( Dae Hyun Lim ),양준영 ( Jun Young Yang ),김소영 ( So Young Kim ),이정선 ( Jung Sun Yi ),염영나 ( Young Na Yum ),임채형 ( Chae Hyung Lim ),이진하 ( Jin Ha Lee ),최기환 ( Ki Hw 한국동물실험대체법학회 2014 동물실험대체법학회지 Vol.8 No.1
To identify mutagenic potential of test substances, in vitro Ames tests are commonly used. Recently revised ICH S2(R1) guideline requires in vivo genotoxicity test if the result of the in vitro test is positive. In addition, a method testing multiple endpoints is required for animal welfare. Therefore we established a flow cytometry-based analysis such as Pig-a gene mutation assay and the micronuclei assay for detection of in vivo genotoxic potential using peripheral blood collected from repeated dose toxicity study. To evaluate these new methods, male Sprague Dawley rats were treated for 3, 14 or 28 days with N-nitro-N-ethylurea (ENU). ENU induced mutations in both reticulocytes (RET) and red blood cells of rats dose-dependently from the Pig-a gene mutation assay. ENU also increased micronucleated reticulocytes frequencies in flow cytometry based micronuclei assay, implying chromosomal damage to hematopoetic cells. These data show that both assays were well established. We additionally evaluated urethane and glycidol for applicability of Pig-a gene mutation assay and in vivo micronuclei assay by flow cytometry. Urethane, compared with vehicle control, did not increase Pig-a gene mutation and micronuclei frequency. Glycidol, compared with vehicle control, did not increase in micronuclei frequency, but Pig-a gene mutation significantly increased in the highest concentration for 28 days. Pig-a gene mutation assay for genotoxicity has many advantages: It can detect mutation in various species including humans, primates and rodents; and is integrated with repeated dose toxicity test without additional usage of animals; and has low spontaneous mutation frequency.