메뉴 건너뛰기




Volumn 55, Issue 8, 2010, Pages 500-506

Making a haplotype catalog with estimated frequencies based on SNP homozygotes

Author keywords

haplotype; haplotype frequency; homozygotes; linkage disequilibrium; single nucleotide polymorphisms

Indexed keywords

ARTICLE; GENE FREQUENCY; GENE LOCATION; GENE STRUCTURE; GENETIC ANALYSIS; HAPLOTYPE; HOMOZYGOSITY; HUMAN; JAPANESE; MAJOR CLINICAL STUDY; POPULATION GENETIC PARAMETERS; QUANTITATIVE STUDY; SINGLE NUCLEOTIDE POLYMORPHISM;

EID: 77957569456     PISSN: 14345161     EISSN: None     Source Type: Journal    
DOI: 10.1038/jhg.2010.56     Document Type: Article
Times cited : (2)

References (40)
  • 2
    • 4344671923 scopus 로고    scopus 로고
    • Variation of gene-based SNPs and linkage disequilibrium patterns in the human genome
    • Tsunoda, T., Lathrop, G. M., Sekine, A., Yamada, R., Takahashi, A., Ohnishi, Y. et al. Variation of gene-based SNPs and linkage disequilibrium patterns in the human genome. Hum. Mol. Genet. 13, 1623-1632 (2004).
    • (2004) Hum. Mol. Genet. , vol.13 , pp. 1623-1632
    • Tsunoda, T.1    Lathrop, G.M.2    Sekine, A.3    Yamada, R.4    Takahashi, A.5    Ohnishi, Y.6
  • 7
    • 0025269067 scopus 로고
    • Inference of haplotypes from PCR-amplified samples of diploid populations
    • Clark, A. G. Inference of haplotypes from PCR-amplified samples of diploid populations. Mol. Biol. Evol. 7, 111-122 (1990).
    • (1990) Mol. Biol. Evol , vol.7 , pp. 111-122
    • Clark, A.G.1
  • 8
    • 0029130796 scopus 로고
    • Maximum-likelihood estimation of molecular haplotype frequencies in a diploid population
    • Excoffier, L. & Slatkin, M. Maximum-likelihood estimation of molecular haplotype frequencies in a diploid population. Mol. Biol. Evol. 12, 921-927 (1995).
    • (1995) Mol. Biol. Evol , vol.12 , pp. 921-927
    • Excoffier, L.1    Slatkin, M.2
  • 9
    • 0035071957 scopus 로고    scopus 로고
    • A new statistical method for haplotype reconstruction from population data
    • Stephens, M., Smith, N. J. & Donnelly, P. A new statistical method for haplotype reconstruction from population data. Am. J. Hum. Genet. 68, 978-989 (2001).
    • (2001) Am. J. Hum. Genet. , vol.68 , pp. 978-989
    • Stephens, M.1    Smith, N.J.2    Donnelly, P.3
  • 10
    • 10044232695 scopus 로고    scopus 로고
    • Algorithms for inferring haplotypes
    • Niu, T. Algorithms for inferring haplotypes. Genet. Epidemiol. 27, 334-347 (2004).
    • (2004) Genet. Epidemiol , vol.27 , pp. 334-347
    • Niu, T.1
  • 11
    • 0036138183 scopus 로고    scopus 로고
    • Bayesian haplotype inference for multiple linked single-nucleotide polymorphisms
    • Niu, T., Qin, Z. S., Xu, X. & Liu, J. S. Bayesian haplotype inference for multiple linked single-nucleotide polymorphisms. Am. J. Hum. Genet. 70, 157-169 (2002).
    • (2002) Am. J. Hum. Genet. , vol.70 , pp. 157-169
    • Niu, T.1    Qin, Z.S.2    Xu, X.3    Liu, J.S.4
  • 12
    • 0037320552 scopus 로고    scopus 로고
    • Estimation of haplotype frequencies, linkage-disequilibrium measures, and combination of haplotype copies in each pool by use of pooled DNA data
    • Ito, T., Chiku, S., Inoue, E., Tomita, M., Morisaki, T., Morisaki, H. et al. Estimation of haplotype frequencies, linkage-disequilibrium measures, and combination of haplotype copies in each pool by use of pooled DNA data. Am. J. Hum. Genet. 72, 384-398 (2003).
    • (2003) Am. J. Hum. Genet. , vol.72 , pp. 384-398
    • Ito, T.1    Chiku, S.2    Inoue, E.3    Tomita, M.4    Morisaki, T.5    Morisaki, H.6
  • 14
    • 62649155943 scopus 로고    scopus 로고
    • A unified approach to genotype imputation and haplotype-phase inference for large data sets of trios and unrelated individuals
    • Browning, B. L. & Browning, S. R. A unified approach to genotype imputation and haplotype-phase inference for large data sets of trios and unrelated individuals. Am. J. Hum. Genet. 84, 210-223 (2009).
    • (2009) Am. J. Hum. Genet. , vol.84 , pp. 210-223
    • Browning, B.L.1    Browning, S.R.2
  • 15
    • 35348817330 scopus 로고    scopus 로고
    • Rapid and accurate haplotype phasing and missingdata inference for whole-genome association studies by use of localized haplotype clustering
    • Browning, S. R. & Browning, B. L. Rapid and accurate haplotype phasing and missingdata inference for whole-genome association studies by use of localized haplotype clustering. Am. J. Hum. Genet. 81, 1084-1097 (2007).
    • (2007) Am. J. Hum. Genet. , vol.81 , pp. 1084-1097
    • Browning, S.R.1    Browning, B.L.2
  • 16
    • 4444383439 scopus 로고    scopus 로고
    • Notes on the maximum likelihood estimation of haplotype frequencies
    • Mano, S., Yasuda, N., Katoh, T., Tounai, K., Inoko, H., Imanishi, T. et al. Notes on the maximum likelihood estimation of haplotype frequencies. Ann. Hum. Genet. 68 (Part 3), 257-264 (2004).
    • (2004) Ann. Hum. Genet. , vol.68 , Issue.3 PART , pp. 257-264
    • Mano, S.1    Yasuda, N.2    Katoh, T.3    Tounai, K.4    Inoko, H.5    Imanishi, T.6
  • 17
    • 0034727107 scopus 로고    scopus 로고
    • An SNP map of the human genome generated by reduced representation shotgun sequencing
    • Altshuler, D., Pollara, V. J., Cowles, C. R., Van Etten, W. J., Baldwin, J., Linton, L. et al. An SNP map of the human genome generated by reduced representation shotgun sequencing. Nature 407, 513-516 (2000).
    • (2000) Nature , vol.407 , pp. 513-516
    • Altshuler, D.1    Pollara, V.J.2    Cowles, C.R.3    Van Etten, W.J.4    Baldwin, J.5    Linton, L.6
  • 18
    • 0032876978 scopus 로고    scopus 로고
    • DbSNP-database for single nucleotide polymorphisms and other classes of minor genetic variation
    • Sherry, S. T., Ward, M. & Sirotkin, K. dbSNP-database for single nucleotide polymorphisms and other classes of minor genetic variation. Genome Res. 9, 677-679 (1999).
    • (1999) Genome Res. , vol.9 , pp. 677-679
    • Sherry, S.T.1    Ward, M.2    Sirotkin, K.3
  • 19
    • 0036956227 scopus 로고    scopus 로고
    • Gene-based SNP discovery as part of the Japanese Millennium Genome Project: Identification of 190 562 genetic variations in the human genome. Single-nucleotide polymorphism
    • Haga, H., Yamada, R., Ohnishi, Y., Nakamura, Y. & Tanaka, T. Gene-based SNP discovery as part of the Japanese Millennium Genome Project: identification of 190 562 genetic variations in the human genome. Single-nucleotide polymorphism. J. Hum. Genet. 47, 605-610 (2002).
    • (2002) J. Hum. Genet. , vol.47 , pp. 605-610
    • Haga, H.1    Yamada, R.2    Ohnishi, Y.3    Nakamura, Y.4    Tanaka, T.5
  • 21
    • 18744407845 scopus 로고    scopus 로고
    • Functional SNPs in the lymphotoxin-alpha gene that are associated with susceptibility to myocardial infarction
    • Ozaki, K., Ohnishi, Y., Iida, A., Sekine, A., Yamada, R., Tsunoda, T. et al. Functional SNPs in the lymphotoxin-alpha gene that are associated with susceptibility to myocardial infarction. Nat. Genet. 32, 650-654 (2002).
    • (2002) Nat. Genet. , vol.32 , pp. 650-654
    • Ozaki, K.1    Ohnishi, Y.2    Iida, A.3    Sekine, A.4    Yamada, R.5    Tsunoda, T.6
  • 22
    • 0042667153 scopus 로고    scopus 로고
    • Functional haplotypes of PADI4, encoding citrullinating enzyme peptidylarginine deiminase 4, are associated with rheumatoid arthritis
    • Suzuki, A., Yamada, R., Chang, X., Tokuhiro, S., Sawada, T., Suzuki, M. et al. Functional haplotypes of PADI4, encoding citrullinating enzyme peptidylarginine deiminase 4, are associated with rheumatoid arthritis. Nat. Genet. 34, 395-402 (2003).
    • (2003) Nat. Genet. , vol.34 , pp. 395-402
    • Suzuki, A.1    Yamada, R.2    Chang, X.3    Tokuhiro, S.4    Sawada, T.5    Suzuki, M.6
  • 23
    • 79959524146 scopus 로고    scopus 로고
    • A haplotype map of the human genome
    • Altshuler, D. A haplotype map of the human genome. Nature 437, 1299-1320 (2005).
    • (2005) Nature , vol.437 , pp. 1299-1320
    • Altshuler, D.1
  • 24
    • 35348983887 scopus 로고    scopus 로고
    • A second generation human haplotype map of over 3.1 million SNPs
    • Frazer, K. A., Ballinger, D. G., Cox, D. R., Hinds, D. A., Stuve, L. L., Gibbs, R. A. et al. A second generation human haplotype map of over 3.1 million SNPs. Nature 449, 851-861 (2007).
    • (2007) Nature , vol.449 , pp. 851-861
    • Frazer, K.A.1    Ballinger, D.G.2    Cox, D.R.3    Hinds, D.A.4    Stuve, L.L.5    Gibbs, R.A.6
  • 25
    • 84969213492 scopus 로고    scopus 로고
    • Genome-wide association study of 14 000 cases of seven common diseases and 3000 shared controls
    • Consortium TWTCC. Genome-wide association study of 14 000 cases of seven common diseases and 3000 shared controls. Nature 447, 661-678 (2007).
    • (2007) Nature , vol.447 , pp. 661-678
    • Consortium, T.W.T.C.C.1
  • 27
    • 27544516082 scopus 로고    scopus 로고
    • Genome-wide definitive haplotypes determined using a collection of complete hydatidiform moles
    • Kukita, Y., Miyatake, K., Stokowski, R., Hinds, D., Higasa, K., Wake, N. et al. Genome-wide definitive haplotypes determined using a collection of complete hydatidiform moles. Genome Res. 15, 1511-1518 (2005).
    • (2005) Genome Res. , vol.15 , pp. 1511-1518
    • Kukita, Y.1    Miyatake, K.2    Stokowski, R.3    Hinds, D.4    Higasa, K.5    Wake, N.6
  • 30
    • 67849083083 scopus 로고    scopus 로고
    • Homozygosity mapper-an interactive approach to homozygosity mapping
    • Web Server issue
    • Seelow, D., Schuelke, M., Hildebrandt, F. & Nurnberg, P. Homozygosity Mapper-an interactive approach to homozygosity mapping. Nucleic Acids Res 37 (Web Server issue), W593-W599 (2009).
    • (2009) Nucleic Acids Res. , vol.37
    • Seelow, D.1    Schuelke, M.2    Hildebrandt, F.3    Nurnberg, P.4
  • 34
    • 33846060603 scopus 로고    scopus 로고
    • D-HaploDB: A database of definitive haplotypes determined by genotyping complete hydatidiform mole samples
    • Database issue
    • Higasa, K., Miyatake, K., Kukita, Y., Tahira, T. & Hayashi, K. D-HaploDB: a database of definitive haplotypes determined by genotyping complete hydatidiform mole samples. Nucleic Acids Res. 35 (Database issue), D685-D689 (2007).
    • (2007) Nucleic Acids Res. , vol.35
    • Higasa, K.1    Miyatake, K.2    Kukita, Y.3    Tahira, T.4    Hayashi, K.5
  • 35
    • 0038315436 scopus 로고    scopus 로고
    • Entropy as a measure for linkage disequilibrium over multilocus haplotype blocks
    • Nothnagel, M., Furst, R. & Rohde, K. Entropy as a measure for linkage disequilibrium over multilocus haplotype blocks. Hum. Hered. 54, 186-198 (2002).
    • (2002) Hum. Hered , vol.54 , pp. 186-198
    • Nothnagel, M.1    Furst, R.2    Rohde, K.3
  • 36
    • 67149138099 scopus 로고    scopus 로고
    • Evaluation of haplotype inference using definitive haplotype data obtained from complete hydatidiform moles, and its significance for the analyses of positively selected regions
    • Higasa, K., Kukita, Y., Kato, K., Wake, N., Tahira, T. & Hayashi, K. Evaluation of haplotype inference using definitive haplotype data obtained from complete hydatidiform moles, and its significance for the analyses of positively selected regions. PLoS Genet. 5, e1000468 (2009).
    • (2009) PLoS Genet. , vol.5
    • Higasa, K.1    Kukita, Y.2    Kato, K.3    Wake, N.4    Tahira, T.5    Hayashi, K.6
  • 37
    • 50249108915 scopus 로고    scopus 로고
    • New correction algorithms for multiple comparisons in case-control multilocus association studies based on haplotypes and diplotype configurations
    • Misawa, K., Fujii, S., Yamazaki, T., Takahashi, A., Takasaki, J., Yanagisawa, M. et al. New correction algorithms for multiple comparisons in case-control multilocus association studies based on haplotypes and diplotype configurations. J. Hum. Genet. 53, 789-801 (2008).
    • (2008) J. Hum. Genet. , vol.53 , pp. 789-801
    • Misawa, K.1    Fujii, S.2    Yamazaki, T.3    Takahashi, A.4    Takasaki, J.5    Yanagisawa, M.6
  • 38
    • 61349137526 scopus 로고    scopus 로고
    • Genome-wide haplotype association study identifies the SLC22A3-LPAL2-LPA gene cluster as a risk locus for coronary artery disease
    • Tregouet, D A., Konig, I R., Erdmann, J., Munteanu, A., Braund, P S., Hall, A S. et al. Genome-wide haplotype association study identifies the SLC22A3-LPAL2-LPA gene cluster as a risk locus for coronary artery disease. Nat. Genet. 41, 283-285 (2009).
    • (2009) Nat. Genet. , vol.41 , pp. 283-285
    • Tregouet, D.A.1    Konig, I.R.2    Erdmann, J.3    Munteanu, A.4    Braund, P.S.5    Hall, A.S.6
  • 39
    • 32444441330 scopus 로고    scopus 로고
    • Multiple rare variants in NPC1L1 associated with reduced sterol absorption and plasma low-density lipoprotein levels
    • Cohen, J C., Pertsemlidis, A., Fahmi, S., Esmail, S., Vega, G L., Grundy, S M. et al. Multiple rare variants in NPC1L1 associated with reduced sterol absorption and plasma low-density lipoprotein levels. Proc. Natl Acad. Sci. USA 103, 1810-1815 (2006).
    • (2006) Proc. Natl. Acad. Sci. USA , vol.103 , pp. 1810-1815
    • Cohen, J.C.1    Pertsemlidis, A.2    Fahmi, S.3    Esmail, S.4    Vega, G.L.5    Grundy, S.M.6
  • 40
    • 0034969437 scopus 로고    scopus 로고
    • Are rare variants responsible for susceptibility to complex diseases?
    • Pritchard, J K. Are rare variants responsible for susceptibility to complex diseases? Am. J. Hum. Genet. 69, 124-137 (2001).
    • (2001) Am. J. Hum. Genet. , vol.69 , pp. 124-137
    • Pritchard, J.K.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.