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Volumn 12, Issue 7, 2011, Pages

Targeted enrichment beyond the consensus coding DNA sequence exome reveals exons with higher variant densities

Author keywords

[No Author keywords available]

Indexed keywords

DNA; MICRORNA;

EID: 79960572198     PISSN: 14747596     EISSN: 1474760X     Source Type: Journal    
DOI: 10.1186/gb-2011-12-7-r68     Document Type: Article
Times cited : (169)

References (52)
  • 4
    • 35748959649 scopus 로고    scopus 로고
    • Microarray-based genomic selection for high-throughput resequencing.
    • 10.1038/nmeth1109, 17934469
    • Okou DT, Steinberg KM, Middle C, Cutler DJ, Albert TJ, Zwick ME. Microarray-based genomic selection for high-throughput resequencing. Nat Methods 2007, 4:907-909. 10.1038/nmeth1109, 17934469.
    • (2007) Nat Methods , vol.4 , pp. 907-909
    • Okou, D.T.1    Steinberg, K.M.2    Middle, C.3    Cutler, D.J.4    Albert, T.J.5    Zwick, M.E.6
  • 11
    • 77951976367 scopus 로고    scopus 로고
    • Massively parallel sequencing of exons on the × chromosome identifies RBM10 as the gene that causes a syndromic form of cleft palate.
    • 10.1016/j.ajhg.2010.04.007, 2868995, 20451169
    • Johnston JJ, Teer JK, Cherukuri PF, Hansen NF, Loftus SK, Chong K, Mullikin JC, Biesecker LG. Massively parallel sequencing of exons on the × chromosome identifies RBM10 as the gene that causes a syndromic form of cleft palate. Am J Hum Genet 2010, 86:743-748. 10.1016/j.ajhg.2010.04.007, 2868995, 20451169.
    • (2010) Am J Hum Genet , vol.86 , pp. 743-748
    • Johnston, J.J.1    Teer, J.K.2    Cherukuri, P.F.3    Hansen, N.F.4    Loftus, S.K.5    Chong, K.6    Mullikin, J.C.7    Biesecker, L.G.8
  • 14
    • 77955084820 scopus 로고    scopus 로고
    • Whole exome sequencing and homozygosity mapping identify mutation in the cell polarity protein GPSM2 as the cause of nonsyndromic hearing loss DFNB82.
    • 10.1016/j.ajhg.2010.05.010, 2896776, 20602914
    • Walsh T, Shahin H, Elkan-Miller T, Lee MK, Thornton AM, Roeb W, Abu Rayyan A, Loulus S, Avraham KB, King MC, Kanaan M. Whole exome sequencing and homozygosity mapping identify mutation in the cell polarity protein GPSM2 as the cause of nonsyndromic hearing loss DFNB82. Am J Hum Genet 2010, 87:90-94. 10.1016/j.ajhg.2010.05.010, 2896776, 20602914.
    • (2010) Am J Hum Genet , vol.87 , pp. 90-94
    • Walsh, T.1    Shahin, H.2    Elkan-Miller, T.3    Lee, M.K.4    Thornton, A.M.5    Roeb, W.6    Abu Rayyan, A.7    Loulus, S.8    Avraham, K.B.9    King, M.C.10    Kanaan, M.11
  • 17
    • 84975742565 scopus 로고    scopus 로고
    • A map of human genome variation from population-scale sequencing.
    • 10.1038/nature09534, 3042601, 20981092, 1000 Genomes Project Consortium
    • 1000 Genomes Project Consortium A map of human genome variation from population-scale sequencing. Nature 2010, 467:1061-1073. 10.1038/nature09534, 3042601, 20981092, 1000 Genomes Project Consortium.
    • (2010) Nature , vol.467 , pp. 1061-1073
  • 20
    • 33846057724 scopus 로고    scopus 로고
    • NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins.
    • (Database issue)
    • Pruitt KD, Tatusova T, Maglott DR. NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res 2007, (35(Database issue)):D61-D65.
    • (2007) Nucleic Acids Res , Issue.35
    • Pruitt, K.D.1    Tatusova, T.2    Maglott, D.R.3
  • 25
    • 0031586003 scopus 로고    scopus 로고
    • Prediction of complete gene structures in human genomic DNA.
    • 10.1006/jmbi.1997.0951, 9149143
    • Burge C, Karlin S. Prediction of complete gene structures in human genomic DNA. J Mol Biol 1997, 268:78-94. 10.1006/jmbi.1997.0951, 9149143.
    • (1997) J Mol Biol , vol.268 , pp. 78-94
    • Burge, C.1    Karlin, S.2
  • 26
    • 40449115745 scopus 로고    scopus 로고
    • CONTRAST: a discriminative, phylogeny-free approach to multiple informant de novo gene prediction.
    • 10.1186/gb-2007-8-12-r269, 2246271, 18096039
    • Gross SS, Do CB, Sirota M, Batzoglou S. CONTRAST: a discriminative, phylogeny-free approach to multiple informant de novo gene prediction. Genome Biol 2007, 8:R269. 10.1186/gb-2007-8-12-r269, 2246271, 18096039.
    • (2007) Genome Biol , vol.8
    • Gross, S.S.1    Do, C.B.2    Sirota, M.3    Batzoglou, S.4
  • 28
    • 33644861212 scopus 로고    scopus 로고
    • ORegAnno: an open access database and curation system for literature-derived promoters, transcription factor binding sites and regulatory variation.
    • 10.1093/bioinformatics/btk027, 16397004
    • Montgomery SB, Griffith OL, Sleumer MC, Bergman CM, Bilenky M, Pleasance ED, Prychyna Y, Zhang X, Jones SJ. ORegAnno: an open access database and curation system for literature-derived promoters, transcription factor binding sites and regulatory variation. Bioinformatics 2006, 22:637-640. 10.1093/bioinformatics/btk027, 16397004.
    • (2006) Bioinformatics , vol.22 , pp. 637-640
    • Montgomery, S.B.1    Griffith, O.L.2    Sleumer, M.C.3    Bergman, C.M.4    Bilenky, M.5    Pleasance, E.D.6    Prychyna, Y.7    Zhang, X.8    Jones, S.J.9
  • 34
    • 79959503826 scopus 로고    scopus 로고
    • The International HapMap Project.
    • The International HapMap Project. Nature 426:789-796.
    • Nature , vol.426 , pp. 789-796
  • 35
    • 4644300141 scopus 로고    scopus 로고
    • Bayesian Markov chain Monte Carlo sequence analysis reveals varying neutral substitution patterns in mammalian evolution.
    • 10.1073/pnas.0404142101, 521089, 15292512
    • Hwang DG, Green P. Bayesian Markov chain Monte Carlo sequence analysis reveals varying neutral substitution patterns in mammalian evolution. Proc Natl Acad Sci USA 2004, 101:13994-14001. 10.1073/pnas.0404142101, 521089, 15292512.
    • (2004) Proc Natl Acad Sci USA , vol.101 , pp. 13994-14001
    • Hwang, D.G.1    Green, P.2
  • 36
    • 0037380022 scopus 로고    scopus 로고
    • Transcription-associated mutational asymmetry in mammalian evolution.
    • 10.1038/ng1103, 12612582
    • Green P, Ewing B, Miller W, Thomas PJ, Green ED. Transcription-associated mutational asymmetry in mammalian evolution. Nat Genet 2003, 33:514-517. 10.1038/ng1103, 12612582.
    • (2003) Nat Genet , vol.33 , pp. 514-517
    • Green, P.1    Ewing, B.2    Miller, W.3    Thomas, P.J.4    Green, E.D.5
  • 38
    • 52649157765 scopus 로고    scopus 로고
    • Substantial biases in ultra-short read data sets from high-throughput DNA sequencing.
    • 10.1093/nar/gkn425, 2532726, 18660515
    • Dohm JC, Lottaz C, Borodina T, Himmelbauer H. Substantial biases in ultra-short read data sets from high-throughput DNA sequencing. Nucleic Acids Res 2008, 36:e105. 10.1093/nar/gkn425, 2532726, 18660515.
    • (2008) Nucleic Acids Res , vol.36
    • Dohm, J.C.1    Lottaz, C.2    Borodina, T.3    Himmelbauer, H.4
  • 39
    • 0028358421 scopus 로고
    • The rate of hydrolytic deamination of 5-methylcytosine in double-stranded DNA.
    • 10.1093/nar/22.6.972, 307917, 8152929
    • Shen JC, Rideout WM, Jones PA. The rate of hydrolytic deamination of 5-methylcytosine in double-stranded DNA. Nucleic Acids Res 1994, 22:972-976. 10.1093/nar/22.6.972, 307917, 8152929.
    • (1994) Nucleic Acids Res , vol.22 , pp. 972-976
    • Shen, J.C.1    Rideout, W.M.2    Jones, P.A.3
  • 40
    • 0029065571 scopus 로고
    • Association of increased spontaneous mutation rates with high levels of transcription in yeast.
    • 10.1126/science.7777859, 7777859
    • Datta A, Jinks-Robertson S. Association of increased spontaneous mutation rates with high levels of transcription in yeast. Science 1995, 268:1616-1619. 10.1126/science.7777859, 7777859.
    • (1995) Science , vol.268 , pp. 1616-1619
    • Datta, A.1    Jinks-Robertson, S.2
  • 41
    • 0035871625 scopus 로고    scopus 로고
    • Increased transcription levels induce higher mutation rates in a hypermutating cell line.
    • Bachl J, Carlson C, Gray-Schopfer V, Dessing M, Olsson C. Increased transcription levels induce higher mutation rates in a hypermutating cell line. J Immunol 2001, 166:5051-5057.
    • (2001) J Immunol , vol.166 , pp. 5051-5057
    • Bachl, J.1    Carlson, C.2    Gray-Schopfer, V.3    Dessing, M.4    Olsson, C.5
  • 42
    • 0038701605 scopus 로고    scopus 로고
    • The birth of an alternatively spliced exon: 3' splice-site selection in Alu exons.
    • 10.1126/science.1082588, 12764196
    • Lev-Maor G, Sorek R, Shomron N, Ast G. The birth of an alternatively spliced exon: 3' splice-site selection in Alu exons. Science 2003, 300:1288-1291. 10.1126/science.1082588, 12764196.
    • (2003) Science , vol.300 , pp. 1288-1291
    • Lev-Maor, G.1    Sorek, R.2    Shomron, N.3    Ast, G.4
  • 43
    • 34748907400 scopus 로고    scopus 로고
    • The birth of new exons: mechanisms and evolutionary consequences.
    • 10.1261/rna.682507, 1986822, 17709368
    • Sorek R. The birth of new exons: mechanisms and evolutionary consequences. Rna 2007, 13:1603-1608. 10.1261/rna.682507, 1986822, 17709368.
    • (2007) Rna , vol.13 , pp. 1603-1608
    • Sorek, R.1
  • 44
    • 0028356158 scopus 로고
    • Alu sequences in the coding regions of mRNA: a source of protein variability.
    • 10.1016/0168-9525(94)90254-2, 8073532
    • Makalowski W, Mitchell GA, Labuda D. Alu sequences in the coding regions of mRNA: a source of protein variability. Trends Genet 1994, 10:188-193. 10.1016/0168-9525(94)90254-2, 8073532.
    • (1994) Trends Genet , vol.10 , pp. 188-193
    • Makalowski, W.1    Mitchell, G.A.2    Labuda, D.3
  • 47
    • 70449879427 scopus 로고    scopus 로고
    • Revealing the hidden relationship between nucleosomes and splicing.
    • Kaplan CD. Revealing the hidden relationship between nucleosomes and splicing. Cell Cycle 2009, 8:3633-3634.
    • (2009) Cell Cycle , vol.8 , pp. 3633-3634
    • Kaplan, C.D.1
  • 49
    • 80053110609 scopus 로고    scopus 로고
    • Nimblegen Capture Protocol for SOLiD Platform.
    • Nimblegen Capture Protocol for SOLiD Platform. , http://www.hgsc.bcm.tmc.edu/cascade-tech-solid_capture_protocol-st.hgsc?pageLocation=solid_capture_protocol
  • 50
    • 70450177746 scopus 로고    scopus 로고
    • BFAST: an alignment tool for large scale genome resequencing.
    • 10.1371/journal.pone.0007767, 2770639, 19907642
    • Homer N, Merriman B, Nelson SF. BFAST: an alignment tool for large scale genome resequencing. PLoS One 2009, 4:e7767. 10.1371/journal.pone.0007767, 2770639, 19907642.
    • (2009) PLoS One , vol.4
    • Homer, N.1    Merriman, B.2    Nelson, S.F.3
  • 51
    • 67649884743 scopus 로고    scopus 로고
    • Fast and accurate short read alignment with Burrows-Wheeler transform.
    • 10.1093/bioinformatics/btp324, 2705234, 19451168
    • Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 2009, 25:1754-1760. 10.1093/bioinformatics/btp324, 2705234, 19451168.
    • (2009) Bioinformatics , vol.25 , pp. 1754-1760
    • Li, H.1    Durbin, R.2
  • 52
    • 84872663439 scopus 로고    scopus 로고
    • Sequence Read Archive.
    • Sequence Read Archive. , http://www.ncbi.nlm.nih.gov/Traces/sra


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