• Journal of Information Processing Systems
• /
• 제14권3호
• /
• pp.655-665
• /
• 2018

In efforts to increase its agricultural productivity, the Indonesian Center for Agricultural Biotechnology and Genetic Resources Research and Development has conducted a variety of genomic studies using high-throughput DNA genotyping and sequencing. The large quantity of data (big data) produced by these biotechnologies require high performance data management system to store, backup, and secure data. Additionally, these genetic studies are computationally demanding, requiring high performance processors and memory for data processing and analysis. Reliable network connectivity with large bandwidth to transfer data is essential as well as database applications and statistical tools that include cleaning, quality control, querying based on specific criteria, and exporting to various formats that are important for generating high yield varieties of crops and improving future agricultural strategies. This manuscript presents a reliable, secure, and scalable information technology infrastructure tailored to Indonesian agriculture genotyping studies.

• Genomics & Informatics
• /
• 제10권3호
• /
• pp.194-199
• /
• 2012

In addition to single-nucleotide polymorphisms (SNP), copy number variation (CNV) is a major component of human genetic diversity. Among many whole-genome analysis platforms, SNP arrays have been commonly used for genomewide CNV discovery. Recently, a number of CNV defining algorithms from SNP genotyping data have been developed; however, due to the fundamental limitation of SNP genotyping data for the measurement of signal intensity, there are still concerns regarding the possibility of false discovery or low sensitivity for detecting CNVs. In this study, we aimed to verify the effect of combining multiple CNV calling algorithms and set up the most reliable pipeline for CNV calling with Affymetrix Genomewide SNP 5.0 data. For this purpose, we selected the 3 most commonly used algorithms for CNV segmentation from SNP genotyping data, PennCNV, QuantiSNP; and BirdSuite. After defining the CNV loci using the 3 different algorithms, we assessed how many of them overlapped with each other, and we also validated the CNVs by genomic quantitative PCR. Through this analysis, we proposed that for reliable CNV-based genomewide association study using SNP array data, CNV calls must be performed with at least 3 different algorithms and that the CNVs consistently called from more than 2 algorithms must be used for association analysis, because they are more reliable than the CNVs called from a single algorithm. Our result will be helpful to set up the CNV analysis protocols for Affymetrix Genomewide SNP 5.0 genotyping data.

• 한국유기농업학회지
• /
• 제12권4호
• /
• pp.451-461
• /
• 2004

In an animals, identification system has been widely used by ear tag with dummy code and blood typing for parernity. Also, genotyping methods were using for useful mean of individual identification for live animals. In the case of genotyping estimation of gene in population of korean native chicken. In this study, we tested for development of genetic markers used it possible to determination of individual identification system. The candidate genetic markers were used already bow 10 of microstalite DNA sequence information in chromosome No. 1 and 14. Result of analysis for genotyping, the number of alleles of those microstatelites DNA was shown minimal 3 to 12 and the heterozygote expression frequency range was shown from 0.617 to 0.862. In our result, effective number of allele for each microsatellites DNA was shown 3~7, and the accuracy of individual identification was shown nearly 100%, when used with 6 genetic marker. This study was about genotyping method for identification used specific genetic marker form microsatellite DNA in the brand marketing of korean native chicken. Our results suggest that genotyping method used specific genetic marker from microsatellite DNA might be very useful for determination of individual identification.

• Translational and Clinical Pharmacology
• /
• 제25권2호
• /
• pp.63-66
• /
• 2017

Allopurinol-induced severe cutaneous adverse reactions (SCARs) such as Stevens-Johnson syndrome (SJS), toxic epidermal necrolysis (TEN), and drug reaction with eosinophilia and systemic symptoms (DRESS) syndrome are reportedly associated with the $HLA-B^{\star}58:01$ genotype. Three patients who developed SCARs after allopurinol administration were subjected to HLA-B genotyping and lymphocyte activation test (LAT) to evaluate genetic risk and to detect the causative agent, respectively. All three patients given allopurinol to treat gout were diagnosed with DRESS syndrome. Symptom onset commenced 7-24 days after drug exposure; the patients took allopurinol (100-200 mg/d) for 2-30 days. HLA-B genotyping was performed using a polymerase chain reaction (PCR)-sequence-based typing (SBT) method. All patients had a single $HLA-B^{\star}58:01$ allele: $HLA-B^{\star}13:02/^{\star}58:01$ (a 63-year-old male), $HLA-B^{\star}48:01/^{\star}58:01$ (a 71-year-old female), and $HLA-B^{\star}44:03/^{\star}58:01$ (a 22-year-old male). Only the last patient yielded a positive LAT result, confirming that allopurinol was the causative agent. These findings suggest that patients with $HLA-B^{\star}58:01$ may develop SCARs upon allopurinol administration. Therefore, HLA-B genotyping could be helpful in preventing serious problems attributable to allopurinol treatment, although PCR-SBT HLA-B genotyping is time consuming. A simple genotyping test is required in practice. LAT may help to identify a causative agent.

• BMB Reports
• /
• 제37권1호
• /
• pp.11-27
• /
• 2004

The introduction of molecular markers in genetic analysis has revolutionized medicine. These molecular markers are genetic variations associated with a predisposition to common diseases and individual variations in drug responses. Identification and genotyping a vast number of genetic polymorphisms in large populations are increasingly important for disease gene identification, pharmacogenetics and population-based studies. Among variations being analyzed, single nucleotide polymorphisms seem to be most useful in large-scale genetic analysis. This review discusses approaches for genetic analysis, use of different markers, and emerging technologies for large-scale genetic analysis where millions of genotyping need to be performed.

• 한국군사과학기술학회지
• /
• 제14권2호
• /
• pp.305-312
• /
• 2011

Bacillus anthracis(Ba) is a Gram-positive spore-forming bacterium that causes the disease anthrax. The feature of Ba is the presence of two large virulence plasmids, pXO1 and pXO2. Molecular genotyping of Ba has been difficult to the lack of polymorphic DNA marker. Ba isolated from Korea has been genotyped using various nucleotide analysis methods, such as 16s rDNA sequencing and multiple-locus variable-number tandem repeat (MLVA) analysis. We identified genotypes that represent a genetic lineage in the B1 cluster. This study emphasized the need to perform molecular genotyping when attempting to verify a strain-specific Ba.

• Journal of Microbiology and Biotechnology
• /
• 제16권2호
• /
• pp.291-294
• /
• 2006

Clostridium perfringens strains were isolated from swine diarrhea in Korea. Three out of nineteen (15.8%) isolates of C. perfringens were found to be enterotoxigenic by PCR analysis. PCR-based genotyping of the three enterotoxigenic isolates of C. perfringens revealed that they were types A, C and D, respectively. These results suggest that various types of enterotoxigenic C. perfringens can cause swine diarrhea, and that the presence of enterotoxigenic type A strain, known to be strongly associated with food poisoning, may cause public health problem in Korea.

• 생명과학회지
• /
• 제24권9호
• /
• pp.1025-1029
• /
• 2014

자궁경부암은 전세계 여성의 사망원인 2위를 차지하며, 인유두종바이러스 감염과 상관성이 있다. 인유두종바이러스의 백신정책, 병인론, 추적관찰, 역학에서 유전형 검사는 중요하다. 후향적 연구를 위하여 파라핀 조직에서 역교잡반응을 이용하여 인유두종바이러스의 유전형을 검사하는 것은 명확하게 증명된 것은 아니다. 본 연구에서는 자궁경부암 파라핀 조직에서 역교잡반응을 사용하여 인유두종바이러스의 유전형 검사의 유용성을 평가하였다. 총 52개의 자궁경부암 파라핀 조직을 사용하여 역교잡반응을 실시하여 인유두종바이러스의 유전형을 검출하였다. 52개의 파라핀 조직중에서 32(61.5%) 건에서 인유두종바이러스가 검출되었으며, 단순감염이 27(84.4%) 건, 복합감염이 5(15.6%) 건으로 검출되었다. 단순감염에서 인유두종바이러스 유전형은 고위험군 18(8), 58(6), 16(5), 33(1), 35(1), 39(1), 56(1) 유전형과, 저위험군 11(2), 6(1), 70(1) 유전형으로 분석되었다. 복합감염에서 인유두종바이러스 유전형은 16/18(2), 18/52(1), 16/56(1), 16/18/33(1) 유전형으로 검출되었다. 본 연구를 통하여, 파라핀 조직으로 후향적 연구를 위한 인유두종바이러스 유전형 검사가 가능할 것으로 기대된다.

• 한국양봉학회지
• /
• 제32권3호
• /
• pp.147-154
• /
• 2017

꿀벌은 화분매개 뿐만 아니라, 양봉산물을 생산하는 주요한 산업곤충 중 하나이다. 최근 농촌진흥청과 예천곤충 연구소에서는 국내 최초로 수밀력 우수 꿀벌 품종인 '장원벌'을 선발하여 보급하고 있다. 본 연구에서는 장원벌 계통 특이 분자 마커 개발을 위해 장원벌 부계인 D계통 특이적인 분자 마커를 개발 하고자 Sequence-Based Genotyping (SBG) 분석을 수행하였다. SGB 분석은 농촌진흥청 국립농업과학원에서 보존 육성중인 A, C, D, E, F 5개 기본종 계통에 대해 수행되었으며, 이를 통해 1,029개 SNP를 확보 할 수 있었다. 이후 A, C, D, F, E 기본종 계통 및 $D{\times}F$ 교배계통에 대한 SNP filtering 및 validation을 통해 최종적으로 AmD6 및 AmD9 두 개의 SNP 마커를 선발 하였으며, genotyping 분석을 통해 AmD9 마커가 장원벌 부계인 D 계통을 100% 구분 할 수 있는 것으로 확인되었다. 본 마커를 통해 D 계통 및 장원벌을 보다 정확하게 판별하고 육종에 활용 할 수 있을 것으로 기대하고 있다.

• Parasites, Hosts and Diseases
• /
• 제54권1호
• /
• pp.15-20
• /
• 2016

Toxoplasmosis is an important zoonotic disease that can cause abortion in humans and animals. The aim of this study was isolation and subsequent genotyping of Toxoplasma gondii isolates in ovine aborted fetuses. During 2012-2013, 39 ovine aborted fetuses were collected from sheep flocks in Khorasan Razavi Province, Iran. The brain samples were screened for detection of the parasite DNA by nested PCR. The positive brain samples were bioassayed in Webster Swiss mice. The serum samples of mice were examined for T. gondii antibodies by IFAT at 6 weeks post inoculation, and T. gondii cysts were searched in brain tissue samples of seropositive mice. The positive samples were genotyped by using a PCR-RLFP method. Subsequently, GRA6 sequences of isolates were analyzed using a phylogenetic method. The results revealed that T. gondii DNA was detected in 54% (20/37, 95% CI 38.4-69.0%) brain samples of ovine aborted fetuses. In bioassay of mice, only 2 samples were virulent and the mice were killed at 30 days post inoculation, while the others were non-virulent to mice. The size of cysts ranged $7-22{\mu}m$. Complete genotyping data for GRA6 locus were observed in 5 of the 20 samples. PCR-RLFP results and phylogenetic analysis revealed that all of the isolated samples were closely related to type I. For the first time, we could genotype and report T. gondii isolates from ovine aborted fetuses in Khorasan Razavi Province, Iran. The results indicate that the T. gondii isolates are genetically related to type I, although most of them were non-virulent for mice.