메뉴 건너뛰기




Volumn 7, Issue 4, 2013, Pages 2229-2248

An empirical bayes testing procedure for detecting variants in analysis of next generation sequencing data

Author keywords

Bayesian FDR; Multiplicity control; Next generation sequencing; Optimality; Variant call

Indexed keywords


EID: 84891543623     PISSN: 19326157     EISSN: 19417330     Source Type: Journal    
DOI: 10.1214/13-AOAS660     Document Type: Article
Times cited : (16)

References (60)
  • 3
    • 77954202495 scopus 로고    scopus 로고
    • A statistical method for the detection of variants from next-generation resequencing of DNA pools
    • Bansal, V. (2010). A statistical method for the detection of variants from next-generation resequencing of DNA pools. Bioinformatics 26 i318-i324.
    • (2010) Bioinformatics , vol.26
    • Bansal, V.1
  • 4
    • 56049099059 scopus 로고    scopus 로고
    • Screening for partial conjunction hypotheses
    • MR2522270
    • Benjamini, Y. and Heller, R. (2008). Screening for partial conjunction hypotheses. Biometrics 64 1215-1222. MR2522270.
    • (2008) Biometrics , vol.64 , pp. 1215-1222
    • Benjamini, Y.1    Heller, R.2
  • 5
    • 0001677717 scopus 로고
    • Controlling the false discovery rate: A practical and powerful approach to multiple testing
    • MR1325392
    • Benjamini, Y. and Hochberg, Y. (1995). Controlling the false discovery rate: A practical and powerful approach to multiple testing. J. R. Stat. Soc. Ser. B Stat. Methodol. 57 289-300. MR1325392.
    • (1995) J.R. Stat. Soc. Ser. B Stat. Methodol , vol.57 , pp. 289-300
    • Benjamini, Y.1    Hochberg, Y.2
  • 6
    • 44349132708 scopus 로고    scopus 로고
    • Common and rare variants in multifactorial susceptibility to common diseases
    • Bodmer, W. and Bonilla, C. (2008). Common and rare variants in multifactorial susceptibility to common diseases. Nat. Genet. 40 695-701.
    • (2008) Nat. Genet , vol.40 , pp. 695-701
    • Bodmer, W.1    Bonilla, C.2
  • 8
    • 84859613736 scopus 로고    scopus 로고
    • Ecological genomics of Anopheles gambiae along a latitudinal cline: A population-resequencing approach
    • Cheng, C., White, B. J., Kamdem, C., Mockaitis, K., Costantini, C., Hahn, M. W. and Besansky, N. J. (2012). Ecological genomics of Anopheles gambiae along a latitudinal cline: A population-resequencing approach. Genetics 190 1417-1432.
    • (2012) Genetics , vol.190 , pp. 1417-1432
    • Cheng, C.1    White, B.J.2    Kamdem, C.3    Mockaitis, K.4    Costantini, C.5    Hahn, M.W.6    Besansky, N.J.7
  • 10
    • 84860364689 scopus 로고    scopus 로고
    • A powerful test for multiple rare variants association studies that incorporates sequencing qualities
    • Daye, Z. J., Li, H. andWei, Z. (2012). A powerful test for multiple rare variants association studies that incorporates sequencing qualities. Nucleic Acids Res. 40 e60.
    • (2012) Nucleic Acids Res , vol.40
    • Daye, Z.J.1    Li, H.2    Wei, Z.3
  • 12
    • 14944366263 scopus 로고    scopus 로고
    • Bayesians, frequentists, and scientists
    • MR2166064
    • Efron, B. (2005). Bayesians, frequentists, and scientists. J. Amer. Statist. Assoc. 100 1-5. MR2166064.
    • (2005) J. Amer. Statist. Assoc , vol.100 , pp. 1-5
    • Efron, B.1
  • 13
    • 47749152434 scopus 로고    scopus 로고
    • Microarrays, empirical Bayes and the two-groups model
    • MR2431866
    • Efron, B. (2008). Microarrays, empirical Bayes and the two-groups model. Statist. Sci. 23 1-22. MR2431866.
    • (2008) Statist. Sci , vol.23 , pp. 1-22
    • Efron, B.1
  • 15
    • 0001398623 scopus 로고
    • Limiting the risk of Bayes and empirical Bayes estimators. I. The Bayes case
    • MR0323014
    • Efron, B. and Morris, C. (1971). Limiting the risk of Bayes and empirical Bayes estimators. I. The Bayes case. J. Amer. Statist. Assoc. 66 807-815. MR0323014.
    • (1971) J. Amer. Statist. Assoc , vol.66 , pp. 807-815
    • Efron, B.1    Morris, C.2
  • 16
    • 84949161149 scopus 로고
    • Stein's estimation rule and its competitors-An empirical Bayes approach
    • MR0388597
    • Efron, B. andMorris, C. (1973). Stein's estimation rule and its competitors-An empirical Bayes approach. J. Amer. Statist. Assoc. 68 117-130. MR0388597.
    • (1973) J. Amer. Statist. Assoc , vol.68 , pp. 117-130
    • Efron, B.1    Morris, C.2
  • 17
    • 84949161141 scopus 로고
    • Data analysis using Stein's estimator and its generalizations
    • Efron, B. andMorris, C. N. (1975). Data analysis using Stein's estimator and its generalizations. J. Amer. Statist. Assoc. 311-319.
    • (1975) J. Amer. Statist. Assoc , pp. 311-319
    • Efron, B.1    Morris, C.N.2
  • 18
    • 1542784653 scopus 로고    scopus 로고
    • Empirical Bayes analysis of a microarray experiment
    • MR1946571
    • Efron, B., Tibshirani, R., Storey, J. D. and Tusher, V. (2001). Empirical Bayes analysis of a microarray experiment. J. Amer. Statist. Assoc. 96 1151-1160. MR1946571.
    • (2001) J. Amer. Statist. Assoc , vol.96 , pp. 1151-1160
    • Efron, B.1    Tibshirani, R.2    Storey, J.D.3    Tusher, V.4
  • 21
    • 62549085618 scopus 로고    scopus 로고
    • Human genetic variation and its contribution to complex traits
    • Frazer, K. A., Murray, S. S., Schork, N. J. and Topol, E. J. (2009). Human genetic variation and its contribution to complex traits. Nat. Rev. Genet. 10 241-251.
    • (2009) Nat. Rev. Genet , vol.10 , pp. 241-251
    • Frazer, K.A.1    Murray, S.S.2    Schork, N.J.3    Topol, E.J.4
  • 22
    • 0036020944 scopus 로고    scopus 로고
    • Operating characteristics and extensions of the false discovery rate procedure
    • MR1924303
    • Genovese, C. andWasserman, L. (2002). Operating characteristics and extensions of the false discovery rate procedure. J. R. Stat. Soc. Ser. B Stat. Methodol. 64 499-517. MR1924303.
    • (2002) J.R. Stat. Soc. Ser. B Stat. Methodol , vol.64 , pp. 499-517
    • Genovese, C.1    Wasserman, L.2
  • 23
    • 38549122239 scopus 로고    scopus 로고
    • International genome project launched
    • Hayden, E. C. (2008). International genome project launched. Nature 451 378-379.
    • (2008) Nature , vol.451 , pp. 378-379
    • Hayden, E.C.1
  • 27
    • 78951483665 scopus 로고    scopus 로고
    • Genomic differentiation between temperate and tropical Australian populations of Drosophila melanogaster
    • Kolaczkowski, B., Kern, A. D., Holloway, A. K. and Begun, D. J. (2011). Genomic differentiation between temperate and tropical Australian populations of Drosophila melanogaster. Genetics 187 245-260.
    • (2011) Genetics , vol.187 , pp. 245-260
    • Kolaczkowski, B.1    Kern, A.D.2    Holloway, A.K.3    Begun, D.J.4
  • 28
    • 79951481957 scopus 로고    scopus 로고
    • Initial impact of the sequencing of the human genome
    • Lander, E. S. (2011). Initial impact of the sequencing of the human genome. Nature 470 187-197.
    • (2011) Nature , vol.470 , pp. 187-197
    • Lander, E.S.1
  • 29
    • 67149117126 scopus 로고    scopus 로고
    • Discovery of rare variants via sequencing: Implications for the design of complex trait association studies
    • Li, B. and Leal, S. M. (2009). Discovery of rare variants via sequencing: Implications for the design of complex trait association studies. PLoS Genet. 5 e1000481.
    • (2009) PLoS Genet , vol.5
    • Li, B.1    Leal, S.M.2
  • 30
    • 55549097836 scopus 로고    scopus 로고
    • Mapping short DNA sequencing reads and calling variants using mapping quality scores
    • Li, H., Ruan, J. andDurbin, R. (2008). Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res. 18 1851-1858.
    • (2008) Genome Res , vol.18 , pp. 1851-1858
    • Li, H.1    Ruan, J.2    Durbin, R.3
  • 32
    • 66449114324 scopus 로고    scopus 로고
    • SNP detection for massively parallel whole-genome resequencing
    • Li, R., Li, Y., Fang, X., Yang, H., Wang, J., Kristiansen, K. and Wang, J. (2009b). SNP detection for massively parallel whole-genome resequencing. Genome Res. 19 1124-1132.
    • (2009) Genome Res , vol.19 , pp. 1124-1132
    • Li, R.1    Li, Y.2    Fang, X.3    Yang, H.4    Wang, J.5    Kristiansen, K.6    Wang, J.7
  • 34
    • 79951475133 scopus 로고    scopus 로고
    • A decade's perspective on DNA sequencing technology
    • Mardis, E. R. (2011). A decade's perspective on DNA sequencing technology. Nature 470 198-203.
    • (2011) Nature , vol.470 , pp. 198-203
    • Mardis, E.R.1
  • 38
    • 84950432453 scopus 로고
    • Parametric empirical Bayes inference: Theory and applications (with discussion)
    • MR0696849
    • Morris, C. N. (1983). Parametric empirical Bayes inference: Theory and applications (with discussion). J. Amer. Statist. Assoc. 78 47-65. MR0696849.
    • (1983) J. Amer. Statist. Assoc , vol.78 , pp. 47-65
    • Morris, C.N.1
  • 39
    • 65249131713 scopus 로고    scopus 로고
    • Rare variants of IFIH1, a gene implicated in antiviral responses, protect against type 1 diabetes
    • Nejentsev, S., Walker, N., Riches, D., Egholm, M. and Todd, J. A. (2009). Rare variants of IFIH1, a gene implicated in antiviral responses, protect against type 1 diabetes. Science 324 387-389.
    • (2009) Science , vol.324 , pp. 387-389
    • Nejentsev, S.1    Walker, N.2    Riches, D.3    Egholm, M.4    Todd, J.A.5
  • 40
    • 1942537073 scopus 로고    scopus 로고
    • DNA pooling as a tool for large-scale association studies in complex traits
    • Norton, N., Williams, N.M., O'Donovan, M. C. and Owen, M. J. (2004). DNA pooling as a tool for large-scale association studies in complex traits. Ann. Med. 36 146-152.
    • (2004) Ann. Med , vol.36 , pp. 146-152
    • Norton, N.1    Williams, N.M.2    O'Donovan, M.C.3    Owen, M.J.4
  • 42
    • 67650034261 scopus 로고    scopus 로고
    • Overlapping pools for high-throughput targeted resequencing
    • Prabhu, S. and Peer, I. (2009). Overlapping pools for high-throughput targeted resequencing. Genome Res. 19 1254-1261.
    • (2009) Genome Res , vol.19 , pp. 1254-1261
    • Prabhu, S.1    Peer, I.2
  • 43
    • 0011026447 scopus 로고
    • Asymptotically subminimax solutions of compound statistical decision problems
    • In, Univ. California Press, Berkeley and Los Angeles. MR0044803
    • Robbins, H. (1951). Asymptotically subminimax solutions of compound statistical decision problems. In Proceedings of the Second Berkeley Symposium on Mathematical Statistics and Probability, 1950 131-148. Univ. California Press, Berkeley and Los Angeles. MR0044803.
    • (1951) Proceedings of the Second Berkeley Symposium on Mathematical Statistics and Probability , vol.1950 , pp. 131-148
    • Robbins, H.1
  • 44
    • 0000033354 scopus 로고
    • An empirical Bayes approach to statistics
    • In, 1954-1955, Vol. I Univ. California Press, Berkeley and Los Angeles. MR0084919
    • Robbins, H. (1956). An empirical Bayes approach to statistics. In Proceedings of the Third Berkeley Symposium on Mathematical Statistics and Probability, 1954-1955, Vol. I 157-163. Univ. California Press, Berkeley and Los Angeles. MR0084919.
    • (1956) Proceedings of the Third Berkeley Symposium on Mathematical Statistics and Probability , pp. 157-163
    • Robbins, H.1
  • 45
    • 55349145983 scopus 로고    scopus 로고
    • A general decision theoretic formulation of procedures controlling FDR and FNR from a Bayesian perspective
    • MR2440399
    • Sarkar, S. K., Zhou, T. and Ghosh, D. (2008). A general decision theoretic formulation of procedures controlling FDR and FNR from a Bayesian perspective. Statist. Sinica 18 925-945. MR2440399.
    • (2008) Statist. Sinica , vol.18 , pp. 925-945
    • Sarkar, S.K.1    Zhou, T.2    Ghosh, D.3
  • 46
  • 48
    • 0345822598 scopus 로고    scopus 로고
    • The positive false discovery rate: A Bayesian interpretation and the q-value
    • MR2036398
    • Storey, J. D. (2003). The positive false discovery rate: A Bayesian interpretation and the q-value. Ann. Statist. 31 2013-2035. MR2036398.
    • (2003) Ann. Statist , vol.31 , pp. 2013-2035
    • Storey, J.D.1
  • 49
    • 35348872772 scopus 로고    scopus 로고
    • Oracle and adaptive compound decision rules for false discovery rate control
    • MR2411657
    • Sun, W. and Cai, T. T. (2007). Oracle and adaptive compound decision rules for false discovery rate control. J. Amer. Statist. Assoc. 102 901-912. MR2411657.
    • (2007) J. Amer. Statist. Assoc , vol.102 , pp. 901-912
    • Sun, W.1    Cai, T.T.2
  • 50
    • 62849107228 scopus 로고    scopus 로고
    • Large-scale multiple testing under dependence
    • MR2649603
    • Sun, W. and Cai, T. T. (2009). Large-scale multiple testing under dependence. J. R. Stat. Soc. Ser. B Stat. Methodol. 71 393-424. MR2649603.
    • (2009) J.R. Stat. Soc. Ser. B Stat. Methodol , vol.71 , pp. 393-424
    • Sun, W.1    Cai, T.T.2
  • 51
    • 79954483579 scopus 로고    scopus 로고
    • Multiple testing for pattern identification, with applications to microarray time-course experiments
    • MR2816703
    • Sun, W. and Wei, Z. (2011). Multiple testing for pattern identification, with applications to microarray time-course experiments. J. Amer. Statist. Assoc. 106 73-88. MR2816703.
    • (2011) J. Amer. Statist. Assoc , vol.106 , pp. 73-88
    • Sun, W.1    Wei, Z.2
  • 52
    • 77649191883 scopus 로고    scopus 로고
    • Population resequencing reveals local adaptation of Arabidopsis lyrata to serpentine soils
    • Turner, T. L., Bourne, E. C., Wettberg, E. J. V., Hu, T. T. and Nuzhdin, S. V. (2010). Population resequencing reveals local adaptation of Arabidopsis lyrata to serpentine soils. Nat. Genet. 42 260-263.
    • (2010) Nat. Genet , vol.42 , pp. 260-263
    • Turner, T.L.1    Bourne, E.C.2    Wettberg, E.J.V.3    Hu, T.T.4    Nuzhdin, S.V.5
  • 53
    • 79953735688 scopus 로고    scopus 로고
    • Population-based resequencing of experimentally evolved populations reveals the genetic basis of body size variation in Drosophila melanogaster
    • Turner, T. L., Stewart, A. D., Fields, A. T., Rice, W. R. and Tarone, A. M. (2011). Population-based resequencing of experimentally evolved populations reveals the genetic basis of body size variation in Drosophila melanogaster. PLoS Genet. 7 e1001336.
    • (2011) PLoS Genet , vol.7
    • Turner, T.L.1    Stewart, A.D.2    Fields, A.T.3    Rice, W.R.4    Tarone, A.M.5
  • 55
    • 84891536098 scopus 로고    scopus 로고
    • Simultaneous set-wise testing under dependence, with applications to genome-wide association studies
    • MR2754747
    • Wang, W., Wei, Z. and Sun, W. (2010). Simultaneous set-wise testing under dependence, with applications to genome-wide association studies. Stat. Interface 3 501-511. MR2754747.
    • (2010) Stat. Interface , vol.3 , pp. 501-511
    • Wang, W.1    Wei, Z.2    Sun, W.3
  • 56
    • 70350664664 scopus 로고    scopus 로고
    • Multiple testing in genome-wide association studies via hidden Markov models
    • Wei, Z., Sun, W., Wang, K. and Hakonarson, H. (2009). Multiple testing in genome-wide association studies via hidden Markov models. Bioinformatics 25 2802-2808.
    • (2009) Bioinformatics , vol.25 , pp. 2802-2808
    • Wei, Z.1    Sun, W.2    Wang, K.3    Hakonarson, H.4
  • 57
    • 80455129691 scopus 로고    scopus 로고
    • SNVer: A statistical tool for variant calling in analysis of pooled or individual next-generation sequencing data
    • Wei, Z., Wang, W., Hu, P., Lyon, G. J. and Hakonarson, H. (2011). SNVer: A statistical tool for variant calling in analysis of pooled or individual next-generation sequencing data. Nucleic Acids Res. 39 e132.
    • (2011) Nucleic Acids Res , vol.39
    • Wei, Z.1    Wang, W.2    Hu, P.3    Lyon, G.J.4    Hakonarson, H.5
  • 58
    • 84864395705 scopus 로고    scopus 로고
    • Optimal false discovery rate control for dependent data
    • Xie, J., Cai, T. T., Maris, J. and Li, H. (2011). Optimal false discovery rate control for dependent data. Stat. Interface 4 417-430.
    • (2011) Stat. Interface , vol.4 , pp. 417-430
    • Xie, J.1    Cai, T.T.2    Maris, J.3    Li, H.4
  • 60
    • 84864832228 scopus 로고    scopus 로고
    • Empirical validation of pooled whole genome population re-sequencing in Drosophila melanogaster
    • Zhu, Y., Bergland, A. O., González, J. and Petrov, D. A. (2012). Empirical validation of pooled whole genome population re-sequencing in Drosophila melanogaster. PLoS ONE 7 e41901.
    • (2012) PLoS ONE , vol.7
    • Zhu, Y.1    Bergland, A.O.2    González, J.3    Petrov, D.A.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.