Difference between revisions of "한국인 햅맵과제"

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<p class="HStyle0"><span style="FONT-SIZE: 12pt; LINE-HEIGHT: 160%; FONT-FAMILY: 휴먼명조,한컴돋움">- TCS: </span><span style="FONT-SIZE: 12pt; LINE-HEIGHT: 160%; FONT-FAMILY: 휴먼명조,한컴돋움">Haplotype Maximum Parsimony Tree construction<br /></span></p>
 
<p class="HStyle0"><span style="FONT-SIZE: 12pt; LINE-HEIGHT: 160%; FONT-FAMILY: 휴먼명조,한컴돋움">- TCS: </span><span style="FONT-SIZE: 12pt; LINE-HEIGHT: 160%; FONT-FAMILY: 휴먼명조,한컴돋움">Haplotype Maximum Parsimony Tree construction<br /></span></p>
 
</span></p>
 
</span></p>
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<p>&nbsp;</p>
 
<p>&nbsp;</p>
 
<p>&nbsp;</p>
 
<p>&nbsp;</p>
 
<p>&nbsp;</p>
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     </tbody>
 
     </tbody>
 
</table>
 
</table>
</span>
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</span><br /><!--StartFragment--><font size="3">&nbsp;</font>
 +
<p class="HStyle0" style="LINE-HEIGHT: 180%; TEXT-ALIGN: left"><span style="FONT-WEIGHT: bold; FONT-SIZE: 12pt; LINE-HEIGHT: 180%; FONT-FAMILY: 휴먼명조,한컴돋움">References</span></p>
 +
<p class="HStyle0" style="LINE-HEIGHT: 180%; TEXT-ALIGN: left"><span style="FONT-WEIGHT: bold; FONT-SIZE: 12pt; LINE-HEIGHT: 180%; FONT-FAMILY: 휴먼명조,한컴돋움"><br /></span></p>
 +
<p class="HStyle0"><span style="FONT-SIZE: 12pt; LINE-HEIGHT: 160%; FONT-FAMILY: 휴먼명조,한컴돋움">Ardlie KG, Kruglyak L, Seielstad M. (2002). Patterns of linkage disequilibrium in the human genome. Nat Rev Genet. (4):299-309. </span></p>
 +
<p class="HStyle0"><span style="FONT-SIZE: 12pt; LINE-HEIGHT: 160%; FONT-FAMILY: 휴먼명조,한컴돋움"><br /></span></p>
 +
<p class="HStyle0"><span style="FONT-SIZE: 12pt; LINE-HEIGHT: 160%; FONT-FAMILY: 휴먼명조,한컴돋움">Cardon LR, Abecasis GR. (2003). Using haplotype blocks to map human complex trait loci. Trends Genet. 19(3):135-40. Review.&nbsp; </span></p>
 +
<p class="HStyle0"><span style="FONT-SIZE: 12pt; LINE-HEIGHT: 160%; FONT-FAMILY: 휴먼명조,한컴돋움"><br /></span></p>
 +
<p class="HStyle0"><span style="FONT-SIZE: 12pt; LINE-HEIGHT: 160%; FONT-FAMILY: 휴먼명조,한컴돋움">Carlson, C. S. et al. (2003). Additional SNPs and linkage-disequilibrium analyses are necessary for wholegenome association studies in humans. Nature Genet. 33, 518&ndash;521.</span></p>
 +
<p class="HStyle0"><span style="FONT-SIZE: 12pt; LINE-HEIGHT: 160%; FONT-FAMILY: 휴먼명조,한컴돋움"><br /></span></p>
 +
<p class="HStyle0"><span style="FONT-SIZE: 12pt; LINE-HEIGHT: 160%; FONT-FAMILY: 휴먼명조,한컴돋움">Clark AG, Nielsen R, Signorovitch J, Matise TC, Glanowski S, Heil J, Winn-Deen ES, Holden AL, Lai E. (2003). Linkage disequilibrium and inference of ancestral recombination in 538 single-nucleotide polymorphism clusters across the human genome. Am J Hum Genet. 73(2):285-300.&nbsp; </span></p>
 +
<p class="HStyle0"><span style="FONT-SIZE: 12pt; LINE-HEIGHT: 160%; FONT-FAMILY: 휴먼명조,한컴돋움"><br /></span></p>
 +
<p class="HStyle0"><span style="FONT-SIZE: 12pt; LINE-HEIGHT: 160%; FONT-FAMILY: 휴먼명조,한컴돋움">Daly, M. J., Rioux, J. D., Schaffner, S. F., Hudson, T. J. and Lander, E. S. (2001). High-resolution haplotype structure in the human genome. Nature Genetics 29, 229&ndash;232.</span></p>
 +
<p class="HStyle0"><span style="FONT-SIZE: 12pt; LINE-HEIGHT: 160%; FONT-FAMILY: 휴먼명조,한컴돋움"><br /></span></p>
 +
<p class="HStyle0"><span style="FONT-SIZE: 12pt; LINE-HEIGHT: 160%; FONT-FAMILY: 휴먼명조,한컴돋움">Dawson E, Abecasis GR, Bumpstead S, Chen Y, Hunt S, Beare DM, Pabial J, Dibling T, Tinsley E, Kirby S, Carter D, Papaspyridonos M, Livingstone S, Ganske R, Lohmussaar E, Zernant J, Tonisson N, Remm M, Magi R, Puurand T, Vilo J, Kurg A, Rice K, Deloukas P, Mott R, Metspalu A, Bentley DR, Cardon LR, Dunham I. (2002). A first-generation linkage disequilibrium map of human chromosome 22. Nature. 418(6897):544-8. </span></p>
 +
<p class="HStyle0"><span style="FONT-SIZE: 12pt; LINE-HEIGHT: 160%; FONT-FAMILY: 휴먼명조,한컴돋움"><br /></span></p>
 +
<p class="HStyle0"><span style="FONT-SIZE: 12pt; LINE-HEIGHT: 160%; FONT-FAMILY: 휴먼명조,한컴돋움">Falush D, Stephens M, Pritchard JK (2003). Inference of population structure: Extensions to linked loci and correlated allele frequencies. Genetics.</span></p>
 +
<p class="HStyle0"><span style="FONT-SIZE: 12pt; LINE-HEIGHT: 160%; FONT-FAMILY: 휴먼명조,한컴돋움"><br /></span></p>
 +
<p class="HStyle0"><span style="FONT-SIZE: 12pt; LINE-HEIGHT: 160%; FONT-FAMILY: 휴먼명조,한컴돋움">Gabriel SB, Schaffner SF, Nguyen H, Moore JM, Roy J, Blumenstiel B, Higgins J, DeFelice M, Lochner A, Faggart M, Liu-Cordero SN, Rotimi C, Adeyemo A, Cooper R, Ward R, Lander ES, Daly MJ, Altshuler D. (2002). The structure of haplotype blocks in the human genome. 296, 2225-2229. </span></p>
 +
<p class="HStyle0"><span style="FONT-SIZE: 12pt; LINE-HEIGHT: 160%; FONT-FAMILY: 휴먼명조,한컴돋움"><br /></span></p>
 +
<p class="HStyle0"><span style="FONT-SIZE: 12pt; LINE-HEIGHT: 160%; FONT-FAMILY: 휴먼명조,한컴돋움">Kang HJ, Choi KO, Kim BD, Kim SS, Kim YJ. (2005). FESD: a Functional Element SNPs </span><span style="FONT-SIZE: 12pt; LINE-HEIGHT: 160%; FONT-FAMILY: 휴먼명조,한컴돋움">Database in human, Nucleic Acids Research, 33, D518-D522.</span><span style="FONT-SIZE: 12pt; LINE-HEIGHT: 160%; FONT-FAMILY: 휴먼명조,한컴돋움"> </span></p>
 +
<p class="HStyle0"><span style="FONT-SIZE: 12pt; LINE-HEIGHT: 160%; FONT-FAMILY: 휴먼명조,한컴돋움"><br /></span></p>
 +
<p class="HStyle0"><span style="FONT-SIZE: 12pt; LINE-HEIGHT: 160%; FONT-FAMILY: 휴먼명조,한컴돋움">Dana C Crawford, Tushar Bhangale, Na Li, Garrett Hellenthal, Mark J Rieder, Deborah A Nickerson &amp; Matthew Stephens. (2004) Evidence for substantial fine-scale variation in recombination rates across the human genome. Nature Genetics, Nat Genet. 36(7):700-706.</span></p>
 +
<p class="HStyle0"><span style="FONT-SIZE: 12pt; LINE-HEIGHT: 160%; FONT-FAMILY: 휴먼명조,한컴돋움"><br /></span></p>
 +
<p class="HStyle0"><span style="FONT-SIZE: 12pt; LINE-HEIGHT: 160%; FONT-FAMILY: 휴먼명조,한컴돋움">Lynn BJ, Stephen PW. (2004). Genetic variation, classification and 'race'. Nature Genetics. 36(11):s28-s33.</span></p>
 +
<p class="HStyle0"><span style="FONT-SIZE: 12pt; LINE-HEIGHT: 160%; FONT-FAMILY: 휴먼명조,한컴돋움"><br /></span></p>
 +
<p class="HStyle0"><span style="FONT-SIZE: 12pt; LINE-HEIGHT: 160%; FONT-FAMILY: 휴먼명조,한컴돋움">Lu X, Niu T, Liu JS. (2003). Haplotype information and linkage disequilibrium mapping for single nucleotide polymorphisms. Genome Res. 13(9):2112-7. </span></p>
 +
<p class="HStyle0"><span style="FONT-SIZE: 12pt; LINE-HEIGHT: 160%; FONT-FAMILY: 휴먼명조,한컴돋움"><br /></span></p>
 +
<p class="HStyle0"><span style="FONT-SIZE: 12pt; LINE-HEIGHT: 160%; FONT-FAMILY: 휴먼명조,한컴돋움">Phillips MS, Lawrence R, Sachidanandam R, Morris AP, Balding DJ, Donaldson MA, Studebaker JF, Ankener WM, Alfisi SV, Kuo FS, Camisa AL, Pazorov V, Scott KE, Carey BJ, Faith J, Katari G, Bhatti HA, Cyr JM, Derohannessian V, Elosua C, Forman AM, Grecco NM, Hock CR, Kuebler JM, Lathrop JA, Mockler MA, Nachtman EP, Restine SL, Varde SA, Hozza MJ, Gelfand CA, Broxholme J, Abecasis GR, Boyce-Jacino MT, Cardon LR. (2003). Chromosome-wide distribution of haplotype blocks and the role of recombination hot spots. Nat Genet. 33(3):382-7.</span></p>
 +
<p class="HStyle0"><span style="FONT-SIZE: 12pt; LINE-HEIGHT: 160%; FONT-FAMILY: 휴먼명조,한컴돋움"><br /></span></p>
 +
<p class="HStyle0"><span style="FONT-SIZE: 12pt; LINE-HEIGHT: 160%; FONT-FAMILY: 휴먼명조,한컴돋움">Pritchard JK, Stephens M, Donnelly P. (2000). Inference of population structure using multilocus genotype data. Genetics, 155:945-959.</span></p>
 +
<p class="HStyle0"><span style="FONT-SIZE: 12pt; LINE-HEIGHT: 160%; FONT-FAMILY: 휴먼명조,한컴돋움"><br /></span></p>
 +
<p class="HStyle0"><span style="FONT-SIZE: 12pt; LINE-HEIGHT: 160%; FONT-FAMILY: 휴먼명조,한컴돋움">Reich DE, Cargill M, Bolk S, Ireland J, Sabeti PC, Richter DJ, Lavery T, Kouyoumjian R, Farhadian SF, Ward R, Lander ES. (2001). Linkage disequilibrium in the human genome. Nature. 411(6834):199-204.&nbsp; </span></p>
 +
<p class="HStyle0"><span style="FONT-SIZE: 12pt; LINE-HEIGHT: 160%; FONT-FAMILY: 휴먼명조,한컴돋움"><br /></span></p>
 +
<p class="HStyle0"><span style="FONT-SIZE: 12pt; LINE-HEIGHT: 160%; FONT-FAMILY: 휴먼명조,한컴돋움">Stumpf MP, Goldstein DB. (2003). Demography, recombination hotspot intensity, and the block structure of linkage disequilibrium. Curr Biol. 13(1):1-8.&nbsp; </span></p>
 +
<p class="HStyle0"><span style="FONT-SIZE: 12pt; LINE-HEIGHT: 160%; FONT-FAMILY: 휴먼명조,한컴돋움"><br /></span></p>
 +
<p class="HStyle0"><span style="FONT-SIZE: 12pt; LINE-HEIGHT: 160%; FONT-FAMILY: 휴먼명조,한컴돋움">Tapper WJ, Maniatis N, Morton NE, Collins A. (2003). A metric linkage disequilibrium map of a human chromosome. Ann Hum Genet. 67(Pt 6):487-94.&nbsp; </span></p>
 +
<p class="HStyle0"><span style="FONT-SIZE: 12pt; LINE-HEIGHT: 160%; FONT-FAMILY: 휴먼명조,한컴돋움"><br /></span></p>
 +
<p class="HStyle0"><span style="FONT-SIZE: 12pt; LINE-HEIGHT: 160%; FONT-FAMILY: 휴먼명조,한컴돋움">The International HapMap Consortium. (2003). The International HapMap Project. Nature. 426(6968):789-96.&nbsp; </span></p>
 +
<p class="HStyle0"><span style="FONT-SIZE: 12pt; LINE-HEIGHT: 160%; FONT-FAMILY: 휴먼명조,한컴돋움"><br /></span></p>
 +
<p class="HStyle0"><span style="FONT-SIZE: 12pt; LINE-HEIGHT: 160%; FONT-FAMILY: 휴먼명조,한컴돋움">The International HapMap Consortium. (2005). A haplotype map of the human genome, Nature 437, 1299-1320.</span></p>
 +
<p class="HStyle0"><span style="FONT-SIZE: 12pt; LINE-HEIGHT: 160%; FONT-FAMILY: 휴먼명조,한컴돋움"><br /></span></p>
 +
<p class="HStyle0"><span style="FONT-SIZE: 12pt; LINE-HEIGHT: 160%; FONT-FAMILY: 휴먼명조,한컴돋움">The International SNPWorking Group. (2001). A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms. Nature 409, 928&ndash;933.</span></p>
 +
<p class="HStyle0"><span style="FONT-SIZE: 12pt; LINE-HEIGHT: 160%; FONT-FAMILY: 휴먼명조,한컴돋움"><br /></span></p>
 +
<p class="HStyle0"><span style="FONT-SIZE: 12pt; LINE-HEIGHT: 160%; FONT-FAMILY: 휴먼명조,한컴돋움">Wheeler D.L., Church D.M., Edgar R., Federhen S., Helmberg W., Madden T.L., Pontius J.U., Schuler G.D., Schriml L.M., Sequeira E, Suzek T.O., Tatusova T.A. and Wagner L. (2004) Database resources of the national center for biotechnology information: update. Nucleic Acids Res., 32, D35-D40. </span></p>
 +
<p class="HStyle0"><span style="FONT-SIZE: 12pt; LINE-HEIGHT: 160%; FONT-FAMILY: 휴먼명조,한컴돋움"><br /></span></p>
 +
<p class="HStyle0"><span style="FONT-SIZE: 12pt; LINE-HEIGHT: 160%; FONT-FAMILY: 휴먼명조,한컴돋움">Zhang K, Sun F, Waterman MS, Chen T. (2003). Haplotype block partition with limited resources and applications to human chromosome 21 haplotype data. Am J Hum Genet. 73(1):63-73.&nbsp;<br /></span></p>

Latest revision as of 08:27, 14 April 2006

 한국인 HapMap 데이터베이스 개발

목표한국인 HapMap 과제에서 생산된 SNP 및 Haplotype 데이터를 D/B로 구축하고 LD 분석방법을 개발하며, 통합적인 HapMap 데이터마이닝 시스템을 구축함

연구내용: 

국내 SNP 및 Haplotype 데이터의 D/B 구축

  •   국내 SNP 및 Haplotype 데이터의 수집 기능 강화
  •   구축 된 D/B의 검색 기능 개선

○ LD 및 기타 분석 프로그램 개발

  •   LD block을 이용한 Population comparison system 개발
  •   자동화된 SNP 및 haplotype 분석 프로그램 개발

각종 유전자정보와 연계된 HapMap 검색 시스템 구축

  •   유전자 별 HapMap 검색 시스템 구축
  •   ENCODE 부위별 HapMap 검색 시스템 구축

○ 통합적인 포탈 시스템 구축

  •   dbSNP 및 International HapMap 데이터의 포탈 기능 구축
  •   자동화된 통합적인 데이터의 포탈 기능 구축 

○ 통합적인 HapMap 데이터마이닝 시스템 구축

  •   인종 간 HapMap 비교 검색 시스템 구축
  •   유전자 및 부위별 HapMap 검색 시스템의 기능 강화


기대효과

과제를 통해 구축된 한국인 HapMap 데이터베이스와 검색시스템은 국내 연구자들이 질병연관 연구를 수행할 때 데이터마이닝 시스템으로 활용되어 암, 당뇨병 등과 같은 복합질병의 유전자를 찾는데 중요한 정보를 제공하게 될 것이며, 궁극적으로는 개인별 맞춤약물개발과 같은 신약개발의 중요한 자료로 이용될 수 있을 것임

 

주요 제공 기능

- Haploview: Haplotype reconstruction, LD Block partition, Tagging SNP prediction, Disease Association

- PHASE: Recombination rate calculation

- TCS: Haplotype Maximum Parsimony Tree construction

 

 

 


엔코드 영역

bSNP에 등록된 모든 SNP와 추가적으로 resequencing을 통해 새로 발굴한 모든 SNP에 대해 보다 조밀한 간격으로 genotyping 실험을 진행하였다. 이 연구에서는 10개의 Hapmap ENCODE 중에서 ENm010 영역을 분석에 사용하였다.

표 1 International HapMap ENCODE 영역

   

Region Name

Chromosome band

Genomic interval

Genotyping group

ENr112

2p16.3

Chr2:51633239..52133238

McGill-GQIC, Perlegen

ENr131 

2q37.1 

Chr2:234778639..235278638 

McGill-GQIC, Perlegen

ENr113 

4q26 

Chr4:118705475..119205474 

Broad, Perlegen

ENm010 

7p15.2 

Chr7:26699793..27199792 

UCSF-WU, Perlegen

ENm013 

7q21.13 

Chr7:89395718..89895717 

Broad, Perlegen

ENm014 

7q31.33 

Chr7:126135436..126632577 

Broad, Perlegen

ENr321

8q24.11 

Chr8:118769628..119269627 

Illumina, Perlegen

ENr232 

9q34.11 

Chr9:127061347..127561346 

Illumina, Perlegen

ENr123 

12q12 

Chr12:38626477..39126476 

BCM, Perlegen

ENr213 

18q12.1 

Chr18:23717221..24217220 

Illumina, Perlegen


 

References


Ardlie KG, Kruglyak L, Seielstad M. (2002). Patterns of linkage disequilibrium in the human genome. Nat Rev Genet. (4):299-309.


Cardon LR, Abecasis GR. (2003). Using haplotype blocks to map human complex trait loci. Trends Genet. 19(3):135-40. Review. 


Carlson, C. S. et al. (2003). Additional SNPs and linkage-disequilibrium analyses are necessary for wholegenome association studies in humans. Nature Genet. 33, 518–521.


Clark AG, Nielsen R, Signorovitch J, Matise TC, Glanowski S, Heil J, Winn-Deen ES, Holden AL, Lai E. (2003). Linkage disequilibrium and inference of ancestral recombination in 538 single-nucleotide polymorphism clusters across the human genome. Am J Hum Genet. 73(2):285-300. 


Daly, M. J., Rioux, J. D., Schaffner, S. F., Hudson, T. J. and Lander, E. S. (2001). High-resolution haplotype structure in the human genome. Nature Genetics 29, 229–232.


Dawson E, Abecasis GR, Bumpstead S, Chen Y, Hunt S, Beare DM, Pabial J, Dibling T, Tinsley E, Kirby S, Carter D, Papaspyridonos M, Livingstone S, Ganske R, Lohmussaar E, Zernant J, Tonisson N, Remm M, Magi R, Puurand T, Vilo J, Kurg A, Rice K, Deloukas P, Mott R, Metspalu A, Bentley DR, Cardon LR, Dunham I. (2002). A first-generation linkage disequilibrium map of human chromosome 22. Nature. 418(6897):544-8.


Falush D, Stephens M, Pritchard JK (2003). Inference of population structure: Extensions to linked loci and correlated allele frequencies. Genetics.


Gabriel SB, Schaffner SF, Nguyen H, Moore JM, Roy J, Blumenstiel B, Higgins J, DeFelice M, Lochner A, Faggart M, Liu-Cordero SN, Rotimi C, Adeyemo A, Cooper R, Ward R, Lander ES, Daly MJ, Altshuler D. (2002). The structure of haplotype blocks in the human genome. 296, 2225-2229.


Kang HJ, Choi KO, Kim BD, Kim SS, Kim YJ. (2005). FESD: a Functional Element SNPs Database in human, Nucleic Acids Research, 33, D518-D522.


Dana C Crawford, Tushar Bhangale, Na Li, Garrett Hellenthal, Mark J Rieder, Deborah A Nickerson & Matthew Stephens. (2004) Evidence for substantial fine-scale variation in recombination rates across the human genome. Nature Genetics, Nat Genet. 36(7):700-706.


Lynn BJ, Stephen PW. (2004). Genetic variation, classification and 'race'. Nature Genetics. 36(11):s28-s33.


Lu X, Niu T, Liu JS. (2003). Haplotype information and linkage disequilibrium mapping for single nucleotide polymorphisms. Genome Res. 13(9):2112-7.


Phillips MS, Lawrence R, Sachidanandam R, Morris AP, Balding DJ, Donaldson MA, Studebaker JF, Ankener WM, Alfisi SV, Kuo FS, Camisa AL, Pazorov V, Scott KE, Carey BJ, Faith J, Katari G, Bhatti HA, Cyr JM, Derohannessian V, Elosua C, Forman AM, Grecco NM, Hock CR, Kuebler JM, Lathrop JA, Mockler MA, Nachtman EP, Restine SL, Varde SA, Hozza MJ, Gelfand CA, Broxholme J, Abecasis GR, Boyce-Jacino MT, Cardon LR. (2003). Chromosome-wide distribution of haplotype blocks and the role of recombination hot spots. Nat Genet. 33(3):382-7.


Pritchard JK, Stephens M, Donnelly P. (2000). Inference of population structure using multilocus genotype data. Genetics, 155:945-959.


Reich DE, Cargill M, Bolk S, Ireland J, Sabeti PC, Richter DJ, Lavery T, Kouyoumjian R, Farhadian SF, Ward R, Lander ES. (2001). Linkage disequilibrium in the human genome. Nature. 411(6834):199-204. 


Stumpf MP, Goldstein DB. (2003). Demography, recombination hotspot intensity, and the block structure of linkage disequilibrium. Curr Biol. 13(1):1-8. 


Tapper WJ, Maniatis N, Morton NE, Collins A. (2003). A metric linkage disequilibrium map of a human chromosome. Ann Hum Genet. 67(Pt 6):487-94. 


The International HapMap Consortium. (2003). The International HapMap Project. Nature. 426(6968):789-96. 


The International HapMap Consortium. (2005). A haplotype map of the human genome, Nature 437, 1299-1320.


The International SNPWorking Group. (2001). A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms. Nature 409, 928–933.


Wheeler D.L., Church D.M., Edgar R., Federhen S., Helmberg W., Madden T.L., Pontius J.U., Schuler G.D., Schriml L.M., Sequeira E, Suzek T.O., Tatusova T.A. and Wagner L. (2004) Database resources of the national center for biotechnology information: update. Nucleic Acids Res., 32, D35-D40.


Zhang K, Sun F, Waterman MS, Chen T. (2003). Haplotype block partition with limited resources and applications to human chromosome 21 haplotype data. Am J Hum Genet. 73(1):63-73.