• Title, Summary, Keyword: Haplotype

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Development of Haplotype Reconstruction System Using Public Resources (공개용 리소스를 활용한 Haplotype 재조합 시스템 개발)

  • Kim, Ki-Bong
    • 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.

Effects of Single Nucleotide Polymorphism Marker Density on Haplotype Block Partition

  • Kim, Sun Ah;Yoo, Yun Joo
    • Genomics & Informatics
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    • v.14 no.4
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    • pp.196-204
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    • 2016
  • Many researchers have found that one of the most important characteristics of the structure of linkage disequilibrium is that the human genome can be divided into non-overlapping block partitions in which only a small number of haplotypes are observed. The location and distribution of haplotype blocks can be seen as a population property influenced by population genetic events such as selection, mutation, recombination and population structure. In this study, we investigate the effects of the density of markers relative to the full set of all polymorphisms in the region on the results of haplotype partitioning for five popular haplotype block partition methods: three methods in Haploview (confidence interval, four gamete test, and solid spine), MIG++ implemented in PLINK 1.9 and S-MIG++. We used several experimental datasets obtained by sampling subsets of single nucleotide polymorphism (SNP) markers of chromosome 22 region in the 1000 Genomes Project data and also the HapMap phase 3 data to compare the results of haplotype block partitions by five methods. With decreasing sampling ratio down to 20% of the original SNP markers, the total number of haplotype blocks decreases and the length of haplotype blocks increases for all algorithms. When we examined the marker-independence of the haplotype block locations constructed from the datasets of different density, the results using below 50% of the entire SNP markers were very different from the results using the entire SNP markers. We conclude that the haplotype block construction results should be used and interpreted carefully depending on the selection of markers and the purpose of the study.

Improved Algorithm for Haplotype Block Partitioning : Application to Human Chromosome 21

  • Na, Kyoung-Rak;Kim, Sang-Jun;Kim, Sung-Kwon
    • Proceedings of the Korean Society for Bioinformatics Conference
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    • pp.229-235
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    • 2003
  • Research of basis technology to construct the human haplotype map is one of active areas in SNP post-genomics research. Identification of haplotype block structure from haplotype data is key step in the haplotype map project. Several algorithms have been proposed for the block identification, including the greedy algorithm, and the dynamic programming based algorithm. This paper analyzed block partitioning method of several algorithm which has been proposed in recent years. HapBlock and HaploBlockFinder are programs used in our experiment.

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Genetic Population Structure and Phylogenetic Relationship of the Large-footed Bat (Myotis macrodactylus) on Jeju Island (제주도 큰발윗수염박쥐(Myotis macrodactylus)의 유전적 집단 구조와 계통 유연관계)

  • Kim, Yoo-Kyung;Park, Su-Gon;Han, Sang-Hoon;Han, Sang-Hyun;Oh, Hong-Shik
    • Journal of Life Science
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    • v.26 no.7
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    • pp.749-757
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    • 2016
  • This study was carried out to reveal the genetic population structure of the Jeju Island population and the phylogenetic relationship of East Asian populations of the large-footed bat (Myotis macrodactylus) based on the genetic polymorphisms of mitochondrial cytochrome B (CYTB) and NADH dehydrogenase subunit 1 (ND1) gene sequences. A total of fourteen and nine haplotypes were found in the CYTB and ND1 sequences from East Asian bats, respectively. Haplotype distribution showed locality specific patterns. The results from ND1 haplotype analysis showed that the Jeju Island population has four haplotypes: the Mt. Halla and Western subpopulations have three ND1 haplotypes, but the Eastern subpopulation has just a single haplotype Nd03, which is commonly found on this island. The neighbor-joining (NJ) tree showed the closer relationship between Jeju Island and Japan rather than that between Jeju and Gangwon-do Province. The divergence time between the maternal ancestor lineages of Japanese and Chinese populations was estimated to be 0.789±0.063 MYBP. The secondary divergence between Jeju and Japanese bats was calculated about to be 0.168±0.013 MYBP. The Jeju population has immigrated to the island at least fifty thousand years ago. In addition, ND1 haplotype analysis suggested that the insular bats have experienced at least two further genetic differentiation events within this island. Consequently, these findings suggested that the results of this study may play a critical role in understanding the phylogenetic relationship among East Asian bat populations of M. macrodactylus. To prepare more explainable information on evolutionary correlation, analysis is still required to examine using expanded samples from China, Russia, and southern parts of the Korean Peninsula.

LD-based Algorithm for Haplotype Block Partitioning (Haplotype 블록 분할을 위한 LD 기반 알고리즘)

  • 나경락;김상준;여상수;김성권
    • Proceedings of the Korean Information Science Society Conference
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    • pp.331-333
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    • 2004
  • 본 연구는 Haplotype 데이터에서 나타나는 별개의 Haplotype의 수를 최소화하는 블록으로 분할하는 방법을 제안한다. Multi-population case인 Haplotype 데이터를 분석하기 위해 패턴의 개수를 최소한으로 줄이는 볼록 분할 방법은 전산학적인 최적해의 의미를 가지게 되며, 이와 더불어 생물학적인 의미를 가지는 블록 경계를 찾기 위해 |D'| 을 계산하고 LD를 분석하였다 분석된 LD는 블록 분할 알고리즘에서 블록 결정 함수로 사용하였으며, 이에 대한 검정은 X$^2$-test를 통해 이루어졌다. 많은 Sample로 구성된 Haplotype 데이터로부터 평균 패턴의 개수를 최소화하고 긴 블록 길이를 가지는 블록 분할의 결과를 얻었다.

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Haplotype Diversity and Gene Flow of the Diamondback Moth, Plutella xylostella(L.) (Lepidoptera: Yponomeutidae), in Korea (배추좀나방(나비목: 집나방과)의 haplotype 다양성과 유전자 이동률)

  • 김익수;배진식;최광호;진병래;이경로;손흥대
    • Korean journal of applied entomology
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    • v.39 no.1
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    • pp.43-52
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    • 2000
  • A portion of mitochondria1 COI gene (438 bp) was sequenced from the sampls of Plutella xylostella from four localities in Korea to investigate the population genetic structure and characteristics by measuring the magnitude of genetic diversity and the degree of gene flow among populations. Thirteen haplotypes ranging in nucleotide divergence 0.3% to 1.4%, were obtained from 21 individuals. The nucleotide divergence was similar to the other related studies, but haplotype diversity was substantially higher (mean h = 0.81). The genetic distance among geographically remote Cheju Island population and the two Kimhae populations, distant 1 lkm to each other, was not statistically significant (p<0.05). Instead, a substantial or high female gene flow was detected (Nm = 2-30). One Hawaiian haplotype of the diamondback moth obtained through GenBank search also was genetically similar to the ones obtained from this study. Collectively, the genetic population structure of the diamondback moth in Korea can be characterized into two aspects. First, the diamondback moths in Korea possesses overall moderate genetic divergence based on a high number of haplotypes. Second, a high haplotype diversity within each population due to the long distance dispersal with a substantial dispersal power and the resultant genetic similarity among geographic populations is characteristic.

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Phylogenetic Analysis using mtDNA D-loop Sequences in Korean Native Ducks (mtDNA D-loop 염기서열 변이를 이용한 토종오리의 계통 분류)

  • Choi, Nu Ri;Seo, Dong Won;Jin, Seon Deok;Sultana, Hasina;Heo, Kang Nyeong;Lee, Jun Heon
    • Korean Journal of Poultry Science
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    • v.41 no.4
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    • pp.235-240
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    • 2014
  • Recently, the consumption of duck meat has been gradually increased in Korea. However, most of the duck breeds in Korea were imported from overseas. Based on the large demands for the breeding stocks of native ducks, a new project for the commercial use of the Korean native ducks has been launched. For the initial investigation of the relationships between Korean native duck (KND) with other duck breeds, the sequences from D-loop control region in mitochondrial DNA (mtDNA) was used. The results from phylogenetic analysis indicated that both KND and White Commercial Duck (WCD) breeds were classified well with wild duck breeds. However, mallard duck was not discriminated well with KND. The haplotype analysis indicated that KND and WCD have eight different haplotypes with eleven SNPs. Three haplotypes (haplotype 1, 3, 4) were shared both in KND and WCD. On the other hand, haplotype 1 was appeared only KND and haplotype 5, 6, 7, 8 were identified only in WCD population. With further verifications, the results presented here can be used for the conservation and commercialization of the Korean native ducks.

Regression Models for Haplotype-Based Association Studies

  • Oh, So-Hee;NamKung, Jung-Hyun;Park, Tae-Sung
    • Genomics & Informatics
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    • v.5 no.1
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    • pp.19-23
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    • 2007
  • In this paper, we provide an overview of statistical models for haplotype-based association studies, and summarize their features based on the design matrix. We classify the design matrix into the two types: direct and indirect. For these two kinds of matrices, we present and compare characteristics using a simple hypothetical example, and a real data set. The motivation behind this study was to provide practitioners with an improved understanding, to facilitate the informed selection of the appropriate haplotype-based model and to improve the interpretability of the models.

Distribution Pattern of cpSSR Variants in Korean Populations of Japanese Red Pine (국내 소나무 집단에 있어서 cpSSR 표지자 변이체의 분포양상)

  • Hong, Yong-Pyo;Kwon, Hae-Yun;Kim, Yong-Yul
    • Journal of Korean Society of Forest Science
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    • v.95 no.4
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    • pp.435-442
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    • 2006
  • A total of 167 peculiar haplotypes confirmed from 28 cpSR variants that were observed in 19 populations of Japanese red pine in Korea through cpSSR marker analysis. Thirteen individuals that showed identical haplotype dispersed evenly in 10 populations, and the average number of effective haplotype within population was 13.37. Estimate of genetic diversity (He) was 0.987 on the basis of cpSSR haplotype variants that was equivalent to or higher than the estimates reported in other studies on some forest tree species. Estimation of genetic diversity (S.I.) on the basis of cpSSR variants composing each haplotype revealed the highest estimate of 1.109 for the population of Gangwon-Yeongwol and the lowest estimate of 0.411 for the population of Gyeongbuk Mungyeong with the average of 0.887. Most of observed cpSSR variants appeared to exist commonly in 19 populations (97.62%), and genetic differentiation of cpSSR variants among populations was turned out to be weak (${\Phi}_{ST}=0.024$). Relatively fast rate of mutation of cpSSR marker might be a major cause for such weak population differentiation. There was no identical haplotype shared between 39 population pairs of 173 pair-wise population pairs. Estimation of genetic distance among 19 populations on the basis of population pairs was also impossible, that might be resulted from restricted migration among 19 populations. Considering the observed distribution patterns of cpSSR variants in addition to the previous studies on I-SSR variants, informations on the present geographic location and genetic status of populations should be considered together for effective sustainable management of the genetic resources of Japanese red pine in Korea.

Geographic Variation and Genetic Diversity between Polluted and Unpolluted Sites of Korean Littorina brevicula(Gastropoda, Littorinidae) Based on the Mitochondrial Cytochrome b Gene Sequence (미토콘드리아 Cytochrome b 유전자의 염기서열 분석을 이용한 한국산 총알고둥(복족강, 총앙고둥과)의 지리적 변이 및 오염.비오염지역간의 유전적 다양성)

  • Suh, Jae-Hwa;Kim, Sook-Jung;Song, Jun-Im
    • Animal Systematics, Evolution and Diversity
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    • v.18 no.1
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    • pp.75-84
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    • 2002
  • MtDNA cyt b gene was used to investigate the geographic variation of 11 populations (106 individuals) of the planktonic developing, periwinkle Littorina brevicula, throughout Eastern, Western, and Southern coastal regions in Korea. The sequence of 500 base pairs and 13 different haplotypes were determined. Haplotype LbA was predominated through the populations studied with frequence of 0.877. Haplotypes were shown different frequencies in each coastal region (0.82, 0.90, and 1.00, respectively). enetic analysis of the 61 individuals of L. brevicula from the polluted and unpolluted sites yielded 8 distinct haplotypes. Haplotype LbA also was most common, and it was shared by 0.872 of frequency among specimens.