메뉴 건너뛰기




Volumn , Issue , 2012, Pages

Design and statistical analysis of pooled next generation sequencing for rare variants

Author keywords

[No Author keywords available]

Indexed keywords


EID: 84867012853     PISSN: 1687952X     EISSN: 16879538     Source Type: Journal    
DOI: 10.1155/2012/524724     Document Type: Article
Times cited : (4)

References (37)
  • 1
    • 53649106195 scopus 로고    scopus 로고
    • Next-generation DNA sequencing
    • 2-s2.0-53649106195 10.1038/nbt1486
    • Shendure J., Ji H., Next-generation DNA sequencing. Nature Biotechnology 2008 26 10 1135 1145 2-s2.0-53649106195 10.1038/nbt1486
    • (2008) Nature Biotechnology , vol.26 , Issue.10 , pp. 1135-1145
    • Shendure, J.1    Ji, H.2
  • 2
    • 72849144434 scopus 로고    scopus 로고
    • Sequencing technologies the next generation
    • 2-s2.0-72849144434 10.1038/nrg2626
    • Metzker M. L., Sequencing technologies the next generation. Nature Reviews Genetics 2010 11 1 31 46 2-s2.0-72849144434 10.1038/nrg2626
    • (2010) Nature Reviews Genetics , vol.11 , Issue.1 , pp. 31-46
    • Metzker, M.L.1
  • 3
    • 44349132708 scopus 로고    scopus 로고
    • Common and rare variants in multifactorial susceptibility to common diseases
    • DOI 10.1038/ng.f.136, PII NGF136
    • Bodmer W., Bonilla C., Common and rare variants in multifactorial susceptibility to common diseases. Nature Genetics 2008 40 6 695 701 2-s2.0-44349132708 10.1038/ng.f.136 (Pubitemid 351748875)
    • (2008) Nature Genetics , vol.40 , Issue.6 , pp. 695-701
    • Bodmer, W.1    Bonilla, C.2
  • 4
    • 33750953227 scopus 로고    scopus 로고
    • Whole-genome re-sequencing
    • DOI 10.1016/j.gde.2006.10.009, PII S0959437X06002085, Genomes and Evolution
    • Bentley D. R., Whole-genome re-sequencing. Current Opinion in Genetics & Development 2006 16 545 552 10.1016/j.gde.2006.10.009 (Pubitemid 44738530)
    • (2006) Current Opinion in Genetics and Development , vol.16 , Issue.6 , pp. 545-552
    • Bentley, D.R.1
  • 6
    • 67650047735 scopus 로고    scopus 로고
    • DNA Sudoku - Harnessing high-throughput sequencing for multiplexed specimen analysis
    • 2-s2.0-67650047735 10.1101/gr.092957.109
    • Erlich Y., Chang K., Gordon A., Ronen R., Navon O., Rooks M., Hannon G. J., DNA Sudoku-Harnessing high-throughput sequencing for multiplexed specimen analysis. Genome Research 2009 19 7 1243 1253 2-s2.0-67650047735 10.1101/gr.092957.109
    • (2009) Genome Research , vol.19 , Issue.7 , pp. 1243-1253
    • Erlich, Y.1    Chang, K.2    Gordon, A.3    Ronen, R.4    Navon, O.5    Rooks, M.6    Hannon, G.J.7
  • 7
    • 78751665708 scopus 로고    scopus 로고
    • The next generation of molecular markers from massively parallel sequencing of pooled DNA samples
    • 2-s2.0-78751665708 10.1534/genetics.110.114397
    • Futschik A., Schlötterer C., The next generation of molecular markers from massively parallel sequencing of pooled DNA samples. Genetics 2010 186 1 207 218 2-s2.0-78751665708 10.1534/genetics.110.114397
    • (2010) Genetics , vol.186 , Issue.1 , pp. 207-218
    • Futschik, A.1    Schlötterer, C.2
  • 8
    • 78049366216 scopus 로고    scopus 로고
    • Identification of rare alleles and their carriers using compressed se(que)nsing
    • 2-s2.0-78049366216 10.1093/nar/gkq675 gkq675
    • Shental N., Amir A., Zuk O., Identification of rare alleles and their carriers using compressed se(que)nsing. Nucleic Acids Research 2010 38 19 e179 2-s2.0-78049366216 10.1093/nar/gkq675 gkq675
    • (2010) Nucleic Acids Research , vol.38 , Issue.19
    • Shental, N.1    Amir, A.2    Zuk, O.3
  • 9
    • 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
    • DOI 10.1086/346116
    • Ito T., Chiku S., Inoue E., Tomita M., Morisaki T., Morisaki H., Kamatani N., Estimation of haplotype frequencies, linkage-disequilibrium measures, and combination of haplotype copies in each pool by use of pooled DNA data. The American Journal of Human Genetics 2003 72 2 384 398 2-s2.0-0037320552 10.1086/346116 (Pubitemid 36194247)
    • (2003) American Journal of Human Genetics , vol.72 , Issue.2 , pp. 384-398
    • Ito, T.1    Chiku, S.2    Inoue, E.3    Tomita, M.4    Morisaki, T.5    Morisaki, H.6    Kamatani, N.7
  • 10
    • 0031889566 scopus 로고    scopus 로고
    • Allele frequency distributions in pooled DNA samples: Applications to mapping complex disease genes
    • Shaw S. H., Carrasquillo M. M., Kashuk C., Puffenberger E. G., Chakravarti A., Allele frequency distributions in pooled DNA samples: applications to mapping complex disease genes. Genome Research 1998 8 2 111 123 2-s2.0-0031889566 (Pubitemid 28121940)
    • (1998) Genome Research , vol.8 , Issue.2 , pp. 111-123
    • Shaw, S.H.1    Carrasquillo, M.M.2    Kashuk, C.3    Puffenberger, E.G.4    Chakravarti, A.5
  • 11
    • 11144314695 scopus 로고    scopus 로고
    • Estimating Haplotype-disease associations with pooled genotype data
    • DOI 10.1002/gepi.20040
    • Zeng D., Lin D. Y., Estimating Haplotype-disease associations with pooled genotype data. Genetic Epidemiology 2005 28 1 70 82 2-s2.0-11144314695 10.1002/gepi.20040 (Pubitemid 40041083)
    • (2005) Genetic Epidemiology , vol.28 , Issue.1 , pp. 70-82
    • Zeng, D.1    Lin, D.Y.2
  • 14
    • 65249131713 scopus 로고    scopus 로고
    • Rare variants of IFIH1, a gene implicated in antiviral responses, protect against type 1 diabetes
    • 2-s2.0-65249131713 10.1126/science.1167728
    • Nejentsev S., Walker N., Riches D., Egholm M., Todd J. A., Rare variants of IFIH1, a gene implicated in antiviral responses, protect against type 1 diabetes. Science 2009 324 5925 387 389 2-s2.0-65249131713 10.1126/science. 1167728
    • (2009) Science , vol.324 , Issue.5925 , pp. 387-389
    • Nejentsev, S.1    Walker, N.2    Riches, D.3    Egholm, M.4    Todd, J.A.5
  • 15
    • 84867007629 scopus 로고    scopus 로고
    • Estimating allele frequency from next-generation sequencing of pooled mitochondrial DNA samples
    • Wang T., Pradhan K., Wong L. J., Ye K., Rohan T. E., Estimating allele frequency from next-generation sequencing of pooled mitochondrial DNA samples. Frontiers in Genetics 2011 2, article 51
    • (2011) Frontiers in Genetics , vol.251
    • Wang, T.1    Pradhan, K.2    Wong, L.J.3    Ye, K.4    Rohan, T.E.5
  • 16
    • 77954198372 scopus 로고    scopus 로고
    • Design of association studies with pooled or un-pooled next-generation sequencing data
    • 2-s2.0-77954198372 10.1002/gepi.20501
    • Kim S. Y., Li Y., Guo Y., Li R., Holmkvist J., Hansen T., Pedersen O., Wang J., Nielsen R., Design of association studies with pooled or un-pooled next-generation sequencing data. Genetic Epidemiology 2010 34 5 479 491 2-s2.0-77954198372 10.1002/gepi.20501
    • (2010) Genetic Epidemiology , vol.34 , Issue.5 , pp. 479-491
    • Kim, S.Y.1    Li, Y.2    Guo, Y.3    Li, R.4    Holmkvist, J.5    Hansen, T.6    Pedersen, O.7    Wang, J.8    Nielsen, R.9
  • 17
    • 77954194389 scopus 로고    scopus 로고
    • Resequencing of pooled DNA for detecting disease associations with rare variants
    • 2-s2.0-77954194389 10.1002/gepi.20502
    • Wang T., Lin C. Y., Rohan T. E., Ye K., Resequencing of pooled DNA for detecting disease associations with rare variants. Genetic Epidemiology 2010 34 5 492 501 2-s2.0-77954194389 10.1002/gepi.20502
    • (2010) Genetic Epidemiology , vol.34 , Issue.5 , pp. 492-501
    • Wang, T.1    Lin, C.Y.2    Rohan, T.E.3    Ye, K.4
  • 18
    • 3843056691 scopus 로고    scopus 로고
    • Multiple rare alleles contribute to low plasma levels of HDL cholesterol
    • DOI 10.1126/science.1099870
    • Cohen J. C., Kiss R. S., Pertsemlidis A., Marcel Y. L., McPherson R., Hobbs H. H., Multiple rare alleles contribute to low plasma levels of HDL cholesterol. Science 2004 305 5685 869 872 2-s2.0-3843056691 10.1126/science.1099870 (Pubitemid 39038422)
    • (2004) Science , vol.305 , Issue.5685 , pp. 869-872
    • Cohen, J.C.1    Kiss, R.S.2    Pertsemlidis, A.3    Marcel, Y.L.4    McPherson, R.5    Hobbs, H.H.6
  • 19
    • 33846014328 scopus 로고    scopus 로고
    • A strategy to discover genes that carry multi-allelic or mono-allelic risk for common diseases: A cohort allelic sums test (CAST)
    • DOI 10.1016/j.mrfmmm.2006.09.003, PII S0027510706002740
    • Morgenthaler S., Thilly W. G., A strategy to discover genes that carry multi-allelic or mono-allelic risk for common diseases: A cohort allelic sums test (CAST). Mutation Research-Fundamental and Molecular Mechanisms of Mutagenesis 2007 615 1-2 28 56 2-s2.0-33846014328 10.1016/j.mrfmmm.2006.09.003 (Pubitemid 46054081)
    • (2007) Mutation Research - Fundamental and Molecular Mechanisms of Mutagenesis , vol.615 , Issue.1-2 , pp. 28-56
    • Morgenthaler, S.1    Thilly, W.G.2
  • 20
    • 50949095168 scopus 로고    scopus 로고
    • Methods for detecting associations with rare variants for common diseases: Application to analysis of sequence data
    • 2-s2.0-50949095168 10.1016/j.ajhg.2008.06.024
    • Li B., Leal S. M., Methods for detecting associations with rare variants for common diseases: application to analysis of sequence data. The American Journal of Human Genetics 2008 83 3 311 321 2-s2.0-50949095168 10.1016/j.ajhg.2008.06.024
    • (2008) The American Journal of Human Genetics , vol.83 , Issue.3 , pp. 311-321
    • Li, B.1    Leal, S.M.2
  • 21
    • 61449168010 scopus 로고    scopus 로고
    • A groupwise association test for rare mutations using a weighted sum statistic
    • 2-s2.0-61449168010 10.1371/journal.pgen.1000384 e1000384
    • Madsen B. E., Browning S. R., A groupwise association test for rare mutations using a weighted sum statistic. PLoS Genetics 2009 5 2 2-s2.0-61449168010 10.1371/journal.pgen.1000384 e1000384
    • (2009) PLoS Genetics , vol.5 , Issue.2
    • Madsen, B.E.1    Browning, S.R.2
  • 22
    • 76649136928 scopus 로고    scopus 로고
    • An evaluation of statistical approaches to rare variant analysis in genetic association studies
    • 2-s2.0-76649136928 10.1002/gepi.20450
    • Morris A. P., Zeggini E., An evaluation of statistical approaches to rare variant analysis in genetic association studies. Genetic Epidemiology 2010 34 2 188 193 2-s2.0-76649136928 10.1002/gepi.20450
    • (2010) Genetic Epidemiology , vol.34 , Issue.2 , pp. 188-193
    • Morris, A.P.1    Zeggini, E.2
  • 25
    • 79958100783 scopus 로고    scopus 로고
    • Adaptive tests for association analysis of rare variants
    • 2-s2.0-79958100783 10.1002/gepi.20586
    • Pan W., Shen X., Adaptive tests for association analysis of rare variants. Genetic Epidemiology 2011 35 5 381 388 2-s2.0-79958100783 10.1002/gepi.20586
    • (2011) Genetic Epidemiology , vol.35 , Issue.5 , pp. 381-388
    • Pan, W.1    Shen, X.2
  • 29
    • 33751114975 scopus 로고    scopus 로고
    • Generalized genomic distance-based regression methodology for multilocus association analysis
    • DOI 10.1086/508346
    • Wessel J., Schork N. J., Generalized genomic distance-based regression methodology for multilocus association analysis. The American Journal of Human Genetics 2006 79 5 792 806 2-s2.0-33751114975 10.1086/508346 (Pubitemid 44763395)
    • (2006) American Journal of Human Genetics , vol.79 , Issue.5 , pp. 792-806
    • Wessel, J.1    Schork, N.J.2
  • 30
    • 40749104728 scopus 로고    scopus 로고
    • A Powerful and Flexible Multilocus Association Test for Quantitative Traits
    • DOI 10.1016/j.ajhg.2007.10.010, PII S0002929708000888
    • Kwee L. C., Liu D., Lin X., Ghosh D., Epstein M. P., A powerful and flexible multilocus association test for quantitative traits. The American Journal of Human Genetics 2008 82 2 386 397 2-s2.0-40749104728 10.1016/j.ajhg.2007.10.010 (Pubitemid 351726104)
    • (2008) American Journal of Human Genetics , vol.82 , Issue.2 , pp. 386-397
    • Kwee, L.C.1    Liu, D.2    Lin, X.3    Ghosh, D.4    Epstein, M.P.5
  • 31
  • 32
    • 0034969437 scopus 로고    scopus 로고
    • Are rare variants responsible for susceptibility to complex diseases?
    • DOI 10.1086/321272
    • Pritchard J. K., Are rare variants responsible for susceptibility to complex diseases? The American Journal of Human Genetics 2001 69 1 124 137 2-s2.0-0034969437 10.1086/321272 (Pubitemid 32614025)
    • (2001) American Journal of Human Genetics , vol.69 , Issue.1 , pp. 124-137
    • Pritchard, J.K.1
  • 33
    • 0027189767 scopus 로고
    • Methods for epidemiologic analyses of multiple exposures: A review and comparative study of maximum-likelihood, preliminary-testing, and Empirical-Bayes regression
    • Greenland S., Methods for epidemiologic analyses of multiple exposures: a review and comparative study of maximum-likelihood, preliminary-testing, and Empirical-Bayes regression. Statistics in Medicine 1993 12 8 717 736 2-s2.0-0027189767 10.1002/sim.4780120802 (Pubitemid 23134303)
    • (1993) Statistics in Medicine , vol.12 , Issue.8 , pp. 717-736
    • Greenland, S.1
  • 34
    • 27844521293 scopus 로고    scopus 로고
    • A shrinkage approach to large-scale covariance matrix estimation and implications for functional genomics
    • 10.2202/1544-6115.1175 2183942
    • Schäfer J., Strimmer K., A shrinkage approach to large-scale covariance matrix estimation and implications for functional genomics. Statistical Applications in Genetics and Molecular Biology 2005 4, article 32 10.2202/1544-6115.1175 2183942
    • (2005) Statistical Applications in Genetics and Molecular Biology , vol.432
    • Schäfer, J.1    Strimmer, K.2
  • 35
    • 36749079336 scopus 로고    scopus 로고
    • So many correlated tests, so little time! Rapid adjustment of P values for multiple correlated tests
    • DOI 10.1086/522036
    • Conneely K. N., Boehnke M., So many correlated tests, so little time! Rapid adjustment of P values for multiple correlated tests. The American Journal of Human Genetics 2007 81 1158 1168 10.1086/522036 (Pubitemid 350211447)
    • (2007) American Journal of Human Genetics , vol.81 , Issue.6 , pp. 1158-1168
    • Conneely, K.N.1    Boehnke, M.2
  • 36
    • 0032714352 scopus 로고    scopus 로고
    • Genomic control for association studies
    • 2-s2.0-0032714352 10.1111/j.0006-341X.1999.00997.x ZBL1059.62640
    • Devlin B., Roeder K., Genomic control for association studies. Biometrics 1999 55 4 997 1004 2-s2.0-0032714352 10.1111/j.0006-341X.1999.00997.x ZBL1059.62640
    • (1999) Biometrics , vol.55 , Issue.4 , pp. 997-1004
    • Devlin, B.1    Roeder, K.2
  • 37
    • 16544380910 scopus 로고    scopus 로고
    • Genomic control to the extreme
    • Author reply p. 31 2-s2.0-16544380910 10.1038/ng1104-1129
    • Devlin B., Bacanu S. A., Roeder K., Genomic control to the extreme. Nature Genetics 2004 36 11 1129 1131. Author reply p. 31 2-s2.0-16544380910 10.1038/ng1104-1129
    • (2004) Nature Genetics , vol.36 , Issue.11 , pp. 1129-1131
    • Devlin, B.1    Bacanu, S.A.2    Roeder, K.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.