• Proceedings of the Korean Information Science Society Conference
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• 2004.04b
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• pp.313-315
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• 2004

SNP(Single Nucleotide Polymorphism)은 생물학적 다양성에 관한 연관성 연구(Association Study)에서 이용되어지고 있다. haplotype을 구하기 위해 genotype data를 Haplotype Reconstruction을 하여 한 가닥씩 분리를 한다. Haplotype Reconstruction의 방법은 생물학적 접근법(molecular method)과, 계산적 접근방법(in-silico method)으로 연구되고 있다 계산적 접근법은 생물학적 접근법에 비해 적은 비용과 시간이 소요되는 장점을 지니지만, phase problem으로 인하여 생물학적 접근법에 비해 정확도가 낮다는 단점을 갖는다. 이런 문제를 해결하기 위한 설러 알고리즘들과 프로그램들이 연구 및 개발되고 있다. 본 논문에서는 현재 개발된 프로그램들에 대해서 다양한 테스트를 통한 각 프로그램의 성능 비교를 하였고, 특성과 문제점을 파악하였다.

• Journal of the Korea Academia-Industrial cooperation Society
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• v.11 no.2
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• pp.720-726
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• 2010

Haplotype-based research has become increasingly important in the field of personalized medicine since the haplotype reflects a set of SNPs (Single Nucleotide Polymorphisms) that are genetically associated and inherited together. Currently, the most widely used application softwares available for haplotype reconstruction, based on in silico method, include PL-EM, Haplotyper, PHASE and HAP. PL-EM, Haplotyper and PHASE are command-line application running on LINUX or Unix system and HAP is a web-based client-server application. This paper deals with an integrated haplotype reconstruction system that have been developed with PL-EM and Haplotyper selected from the accuracy test with experimentally verified data on public application softwares. This integrated system is a kind of client-sever one with user friendly web interface and can provide end-users with a high quality of haplotype analysis. SNPs genotype data with a length of 5 derived from 5 people and SNPs genotype data with a length of 13 derived from 15 people were used to test the analysis results of Haplotyper and PL-EM respectively. As a result, this system has been confirmed to provide the systematic and easy-to-understand analysis results that consist of two main parts, i.e. individual haplotype information and haplotype pool information. In this respect, the integration system will be utilized as a useful tool for the discovery of disease related genes and the development of personalized drugs through facilitating the reconstruction of haplotype maps.

• The KIPS Transactions:PartB
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• v.16B no.2
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• pp.157-161
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• 2009

Minimum Letter Flips(MLF) and Weighted Minimum Letter Flips(WMLF) can perform the haplotype reconstruction more accurately from SNP fragments when they have many errors and gaps by introducing the related genotype information. And it is known that WMLF is more accurate in haplotype reconstruction than those based on the MLF. In the paper, we analyze two models under the conditions that the different rates of homozygous site in the genotype information and the different confidence levels according to the sequencing quality. We compare the performance of the two models using neural network and genetic algorithm. If the rate of homozygous site is high and sequencing quality is good, the results of experiments indicate that WMLF/GI has higher accuracy of haplotype reconstruction than that of the MCIH especially when the error rate and gap rate of SNP fragments are high.

• Genomics & Informatics
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• v.2 no.2
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• pp.107-109
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• 2004

HapAnalyzer is an analysis system that provides minimum analysis methods for the SNP-based association studies. It consists of Hardy-Weinberg equilibrium (HWE) test, linkage disequilibrium (LD) computation, haplotype reconstruction, and SNP (or haplotype)-phenotype association assessment. It is well suited to a case-control association study for the unrelated population.

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2004.11a
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• pp.279-285
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• 2004

In the disease association study, the tagSNP selection problem is important at the view of time and cost. We developed the new tagSNP selection system that has also facilities for the haplotype reconstruction and missing data processing. In our system, we improved biological meanings using LD coefficients as well as dynamic programming method. And our system has capability of processing large -scale dataset, such as the total SNPs on a chromosome. We have tested our system with various dataset from daly et al., patil et al., HapMap Project, artificial dataset, and so on.

• Journal of KIISE:Computer Systems and Theory
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• v.35 no.11
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• pp.509-516
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• 2008

The Minimum Letter Flips (MLF) model and the Weighted Minimum Letter Flips (WMLF) model are for solving the haplotype assembly problem. But these two models are effective only when the error rate in SNP fragments is low. In this paper, we first establish a new computational model that employs the related genotype information as an improvement of the WMLF model and show its NP-hardness, and then propose an efficient genetic algorithm to solve the haplotype assembly problem. The results of experiments on random data set and a real data set indicate that the introduction of genotype information to the WMLF model is quite effective in improving the reconstruction rate especially when the error rate in SNP fragments is high. And the results also show that genotype information increases the convergence speed of the genetic algorithm.

• Proceedings of the Korean Information Science Society Conference
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• 2005.07b
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• pp.271-273
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• 2005

유전자 분석기술의 발전은 지놈 프로젝트(genome project)와 햅맵 프로젝트(hapmap project)를 가능하게 하였으며 이제는 맞춤형 진단 및 신약 개발 등 실제 사업의 구체화를 가져오게 하였다. 실제 사업에 적용시키기 위해서는 비용 절감의 문제를 해결해야 한다. 그래서 대용량의 유전자형(genotype)데이터를 정확하고 빠르게 일배체형(haplotype)으로 재구성해 줄 수 있는 시스템이 생물 산업 및 제약 산업에서 제기되어 지고 있다. 기존의 연구에서 비록 정확성이 높은 알고리즘들이 개발되어 있지만 기존의 방법들은 계산에 필요한 양이 크기 때문에 대용량 데이터에 대한 처리가 불가능하였다. 우리가 제안하는 시스템은 대용량 데이터를 유동적인 크기로 블록을 분할하여 대용량 데이터 처리 문제를 해결하였다. 또한 나누어진 블록에서 나타나는 모호한 이형접합체(heterozygote)의 위상(phase)의 결정 과정에 LD기반의 블록 분할 방법을 이용함으로써, 추론된 결과의 정확률을 높였다. 구현된 시스템의 성능평가는 ms로 구성한 인공데이터를 사용하여 수행하였다.

• Clinical and Experimental Pediatrics
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• v.48 no.5
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• pp.495-499
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• 2005

Purpose : Interleukin-4(IL-4) is a critical component of the Th2 cytokine pathway and contributes to severity of respiratory syncytial virus(RSV) bronchiolitis. Previous studies observed an association between severe RSV bronchiolitis in Korean children with a common haplotype of the IL4 promoter. This study was performed to investigate functional differences of the variant IL4 promoter haplotypes. Methods : Genomic DNA was obtained from 20 children from 6 to 48 months of age in the Department of Pediatrics, Seoul National University Bundang Hospital. The IL4 promoter spanning an 1.2 kb region was amplified and haplotype was determined by cloning and the PHASE reconstruction. Transcriptional activity of Jurkat T cells which were transfected with each IL4 haplotype were analyzed by use of luciferase assay. Results : Three haplotypes of the IL4 promoter have been identified with the frequency of GCC(7 percent), TCC(17 percent), and TTT(76 percent). The TTT haplotype demonstrated the highest luciferase values in both unstimulated and PMA-stimulated Jurkat T cells. Increases in transcriptional activity compared to GCC have been shown in TTT(5.3 fold higher) followed by TCC(4.2 fold higher) in unstimulated Jurkat T cells. Conclusion : We provided evidence that increased transcriptional activity of the TTT haplotype of the IL4 promoter, which has previously been over-represented in Korean children with severe RSV bronchiolitis. Therefore, IL-4 could play a potential role in the pathogenesis of RSV infection, possibly via an altered transcriptional activity of the different IL4 haplotypes.

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2003.10a
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• pp.221-228
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• 2003

This paper presents a novel method that can identify the individual's haplotype from the given genotypes. Because of the limitation of the conventional single-locus analysis, haplotypes have gained increasing attention in the mapping of complex-disease genes. Conventionally there are two approaches which resolve the individual's haplotypes. One is the molecular haplotypings which have many potential limitations in cost and convenience. The other is the in-silico haplotypings which phase the haplotypes from the diploid genotyped populations, and are cost effective and high-throughput method. In-silico haplotyping is divided into two sub-categories - statistical and computational method. The former computes the frequencies of the common haplotypes, and then resolves the individual's haplotypes. The latter directly resolves the individual's haplotypes using the perfect phylogeny model first proposed by Dan Gusfield [7]. Our method combines two approaches in order to increase the accuracy and the running time. The individuals' haplotypes are resolved by considering the MLE (Maximum Likelihood Estimation) in the process of computing the frequencies of the common haplotypes.

• Mycobiology
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• v.50 no.2
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• pp.132-141
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• 2022

Amylomyces rouxii is commonly found as amylolytic fungi in tapai fermentation. However, its diversity is rarely reported despite being often used for food production in Southeast Asia. This research aims to analyze the genetic diversity and the distribution pattern of A. rouxii from Ragi tapai in Java Island, Indonesia. We isolated the fungus from samples obtained from Ragi tapai producing centers in Bandung, Sumedang, Muntilan, Blora, Yogyakarta, and Bondowoso. The obtained isolates were molecularly identified based on the ribosomal regions ITS1/ITS2 and D1/D2, then analyzed for phylogenetic tree reconstruction, genetic distance, genetic variation, and haplotype networking. Six isolates showed specific morphological traits of A. rouxii. However, phylogenetic tree reconstruction on the ribosomal genes showed that the isolates were grouped into two different clades related to two species. Clade A included BDG, SMD, and MTL isolates related to A. rouxii, whereas clade B included YOG, BLR, and BDS isolates related to Mucor indicus. The genetic distances between clades for ITS1/ITS2 and D1/D2 were 0.6145 and 0.1556, respectively. In conclusion, we confirmed the genetic diversity of molds from Ragi tapai in Java Island and showed that the isolates are not only related to A. rouxii as reported before.