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Volumn 6, Issue , 2015, Pages

Analysis of deletion breakpoints from 1,092 humans reveals details of mutation mechanisms

(14)  Abyzov, Alexej a,b,c   Li, Shantao b,d   Kim, Daniel Rhee d   Mohiyuddin, Marghoob e   Stütz, Adrian M f   Parrish, Nicholas F g   Mu, Xinmeng Jasmine b,c   Clark, Wyatt b,c   Chen, Ken h   Hurles, Matthew i   Korbel, Jan O f,j   Lam, Hugo Y K e   Lee, Charles k   Gerstein, Mark B b,c,d  


Author keywords

[No Author keywords available]

Indexed keywords

DEOXYRIBONUCLEASE; HISTONE; NUCLEOTIDE; CHROMATIN; DNA;

EID: 84931292199     PISSN: None     EISSN: 20411723     Source Type: Journal    
DOI: 10.1038/ncomms8256     Document Type: Article
Times cited : (65)

References (57)
  • 1
    • 31144469134 scopus 로고    scopus 로고
    • Structural variation in the human genome
    • Feuk, L., Carson, A. R. & Scherer, S. W. Structural variation in the human genome. Nat. Rev. Genet. 7, 85-97 (2006).
    • (2006) Nat. Rev. Genet. , vol.7 , pp. 85-97
    • Feuk, L.1    Carson, A.R.2    Scherer, S.W.3
  • 3
    • 77950461601 scopus 로고    scopus 로고
    • Origins and functional impact of copy number variation in the human genome
    • Conrad, D. et al. Origins and functional impact of copy number variation in the human genome. Nature 464, 704-712 (2009).
    • (2009) Nature , vol.464 , pp. 704-712
    • Conrad, D.1
  • 4
    • 77949831756 scopus 로고    scopus 로고
    • Structural variation in the human genome and its role in disease
    • Stankiewicz, P. & Lupski, J. R. Structural variation in the human genome and its role in disease. Annu. Rev. Med. 61, 437-455 (2010).
    • (2010) Annu. Rev. Med. , vol.61 , pp. 437-455
    • Stankiewicz, P.1    Lupski, J.R.2
  • 5
    • 68649123353 scopus 로고    scopus 로고
    • Duplication hotspots, rare genomic disorders, and common disease
    • Mefford, H. C. & Eichler, E. E. Duplication hotspots, rare genomic disorders, and common disease. Curr. Opin. Genet. Dev. 19, 196-204 (2009).
    • (2009) Curr. Opin. Genet. Dev. , vol.19 , pp. 196-204
    • Mefford, H.C.1    Eichler, E.E.2
  • 6
    • 77954657070 scopus 로고    scopus 로고
    • Functional impact of global rare copy number variation in autism spectrum disorders
    • Pinto, D. et al. Functional impact of global rare copy number variation in autism spectrum disorders. Nature 466, 368-372 (2010).
    • (2010) Nature , vol.466 , pp. 368-372
    • Pinto, D.1
  • 7
    • 34247481814 scopus 로고    scopus 로고
    • Strong association of de novo copy number mutations with autism
    • Sebat, J. et al. Strong association of de novo copy number mutations with autism. Science 316, 445-449 (2007).
    • (2007) Science , vol.316 , pp. 445-449
    • Sebat, J.1
  • 8
    • 70350626873 scopus 로고    scopus 로고
    • Microduplications of 16p11.2 are associated with schizophrenia
    • McCarthy, S. E. et al. Microduplications of 16p11.2 are associated with schizophrenia. Nat. Genet. 41, 1223-1227 (2009).
    • (2009) Nat. Genet. , vol.41 , pp. 1223-1227
    • McCarthy, S.E.1
  • 9
    • 77950405093 scopus 로고    scopus 로고
    • Genome-wide association study of CNVs in 16,000 cases of eight common diseases and 3,000 shared controls
    • Wellcome Trust Case Control Consortium et al. Genome-wide association study of CNVs in 16,000 cases of eight common diseases and 3,000 shared controls. Nature 464, 713-720 (2010).
    • (2010) Nature , vol.464 , pp. 713-720
    • Wellcome Trust Case Control Consortium et al.1
  • 10
    • 50449091647 scopus 로고    scopus 로고
    • Deletion polymorphism upstream of IRGM associated with altered IRGM expression and Crohn's disease
    • McCarroll, S. A. et al. Deletion polymorphism upstream of IRGM associated with altered IRGM expression and Crohn's disease. Nat. Genet. 40, 1107-1112 (2008).
    • (2008) Nat. Genet. , vol.40 , pp. 1107-1112
    • McCarroll, S.A.1
  • 11
    • 34547664096 scopus 로고    scopus 로고
    • Genomic disorders: Molecular mechanisms for rearrangements and conveyed phenotypes
    • Lupski, J. R. & Stankiewicz, P. Genomic disorders: molecular mechanisms for rearrangements and conveyed phenotypes. PLoS Genet. 1, e49 (2005).
    • (2005) PLoS Genet. , vol.1 , pp. e49
    • Lupski, J.R.1    Stankiewicz, P.2
  • 12
    • 37349109667 scopus 로고    scopus 로고
    • A DNA replication mechanism for generating nonrecurrent rearrangements associated with genomic disorders
    • Lee, J. A., Carvalho, C. M. B. & Lupski, J. R. A DNA replication mechanism for generating nonrecurrent rearrangements associated with genomic disorders. Cell 131, 1235-1247 (2007).
    • (2007) Cell , vol.131 , pp. 1235-1247
    • Lee, J.A.1    Carvalho, C.M.B.2    Lupski, J.R.3
  • 13
    • 67649878596 scopus 로고    scopus 로고
    • The DNA replication FoSTeS/MMBIR mechanism can generate genomic, genic and exonic complex rearrangements in humans
    • Zhang, F. et al. The DNA replication FoSTeS/MMBIR mechanism can generate genomic, genic and exonic complex rearrangements in humans. Nat. Genet. 41, 849-853 (2009).
    • (2009) Nat. Genet. , vol.41 , pp. 849-853
    • Zhang, F.1
  • 14
    • 74049093136 scopus 로고    scopus 로고
    • Nucleotide-resolution analysis of structural variants using BreakSeq and a breakpoint library
    • Lam, H. Y. K. et al. Nucleotide-resolution analysis of structural variants using BreakSeq and a breakpoint library. Nat. Biotechnol. 28, 47-55 (2010).
    • (2010) Nat. Biotechnol. , vol.28 , pp. 47-55
    • Lam, H.Y.K.1
  • 15
    • 79251493015 scopus 로고    scopus 로고
    • A human genome structural variation sequencing resource reveals insights into mutational mechanisms
    • Kidd, J. M. et al. A human genome structural variation sequencing resource reveals insights into mutational mechanisms. Cell 143, 837-847 (2010).
    • (2010) Cell , vol.143 , pp. 837-847
    • Kidd, J.M.1
  • 16
    • 77951700086 scopus 로고    scopus 로고
    • Mutation spectrum revealed by breakpoint sequencing of human germline CNVs
    • Conrad, D. F. et al. Mutation spectrum revealed by breakpoint sequencing of human germline CNVs. Nat. Genet. 42, 385-391 (2010).
    • (2010) Nat. Genet. , vol.42 , pp. 385-391
    • Conrad, D.F.1
  • 17
    • 84975804424 scopus 로고    scopus 로고
    • Mapping copy number variation by population-scale genome sequencing
    • Mills, R. E. et al. Mapping copy number variation by population-scale genome sequencing. Nature 470, 59-65 (2011).
    • (2011) Nature , vol.470 , pp. 59-65
    • Mills, R.E.1
  • 18
    • 79960914208 scopus 로고    scopus 로고
    • Extensive genomic and transcriptional diversity identified through massively parallel DNA and RNA sequencing of eighteen Korean individuals
    • Ju, Y. S. et al. Extensive genomic and transcriptional diversity identified through massively parallel DNA and RNA sequencing of eighteen Korean individuals. Nat. Genet. 43, 745-752 (2011).
    • (2011) Nat. Genet. , vol.43 , pp. 745-752
    • Ju, Y.S.1
  • 19
    • 84865790047 scopus 로고    scopus 로고
    • An integrated encyclopedia of DNA elements in the human genome
    • ENCODE Project Consortium et al. An integrated encyclopedia of DNA elements in the human genome. Nature 489, 57-74 (2012).
    • (2012) Nature , vol.489 , pp. 57-74
    • ENCODE Project Consortium et al.1
  • 20
    • 84862263248 scopus 로고    scopus 로고
    • The NIH Roadmap Epigenomics Program data resource
    • Chadwick, L. H. The NIH Roadmap Epigenomics Program data resource. Epigenomics 4, 317-324 (2012).
    • (2012) Epigenomics , vol.4 , pp. 317-324
    • Chadwick, L.H.1
  • 21
    • 84975795680 scopus 로고    scopus 로고
    • An integrated map of genetic variation from 1,092 human genomes
    • Genomes Project Consortium et al. An integrated map of genetic variation from 1,092 human genomes. Nature 491, 56-65 (2012).
    • (2012) Nature , vol.491 , pp. 56-65
    • 1000 Genomes Project Consortium et al.1
  • 22
    • 84893695366 scopus 로고    scopus 로고
    • TIGRA: A targeted iterative graph routing assembler for breakpoint assembly
    • Chen, K. et al. TIGRA: a targeted iterative graph routing assembler for breakpoint assembly. Genome Res. 24, 310-317 (2014).
    • (2014) Genome Res. , vol.24 , pp. 310-317
    • Chen, K.1
  • 23
    • 79951961326 scopus 로고    scopus 로고
    • AGE: Defining breakpoints of genomic structural variants at single-nucleotide resolution, through optimal alignments with gap excision
    • Abyzov, A. & Gerstein, M. AGE: defining breakpoints of genomic structural variants at single-nucleotide resolution, through optimal alignments with gap excision. Bioinformatics 27, 595-603 (2011).
    • (2011) Bioinformatics , vol.27 , pp. 595-603
    • Abyzov, A.1    Gerstein, M.2
  • 24
    • 84873081003 scopus 로고    scopus 로고
    • Mechanisms of formation of structural variation in a fully sequenced human genome
    • Pang, A. W. C., Migita, O., MacDonald, J. R., Feuk, L. & Scherer, S. W. Mechanisms of formation of structural variation in a fully sequenced human genome. Hum. Mutat. 34, 345-354 (2013).
    • (2013) Hum. Mutat. , vol.34 , pp. 345-354
    • Pang, A.W.C.1    Migita, O.2    Macdonald, J.R.3    Feuk, L.4    Scherer, S.W.5
  • 25
    • 77952296952 scopus 로고    scopus 로고
    • Towards a comprehensive structural variation map of an individual human genome
    • Pang, A. W. et al. Towards a comprehensive structural variation map of an individual human genome. Genome Biol. 11, R52 (2010).
    • (2010) Genome Biol. , vol.11 , pp. R52
    • Pang, A.W.1
  • 26
    • 17444413395 scopus 로고    scopus 로고
    • Alu retrotransposition-mediated deletion
    • Callinan, P. A. et al. Alu retrotransposition-mediated deletion. J. Mol. Biol. 348, 791-800 (2005).
    • (2005) J. Mol. Biol. , vol.348 , pp. 791-800
    • Callinan, P.A.1
  • 27
    • 0024403721 scopus 로고
    • Restriction fragment length polymorphism caused by a deletion involving Alu sequences within the human alpha 2-plasmin inhibitor gene
    • Miura, O., Sugahara, Y., Nakamura, Y., Hirosawa, S. & Aoki, N. Restriction fragment length polymorphism caused by a deletion involving Alu sequences within the human alpha 2-plasmin inhibitor gene. Biochemistry 28, 4934-4938 (1989).
    • (1989) Biochemistry , vol.28 , pp. 4934-4938
    • Miura, O.1    Sugahara, Y.2    Nakamura, Y.3    Hirosawa, S.4    Aoki, N.5
  • 28
    • 84857956783 scopus 로고    scopus 로고
    • Detecting and annotating genetic variations using the HugeSeq pipeline
    • Lam, H. Y. K. et al. Detecting and annotating genetic variations using the HugeSeq pipeline. Nat. Biotechnol. 30, 226-229 (2012).
    • (2012) Nat. Biotechnol. , vol.30 , pp. 226-229
    • Lam, H.Y.K.1
  • 29
    • 84931271931 scopus 로고    scopus 로고
    • VarSim: A high-fidelity simulation and validation framework for high-throughput genome sequencing with cancer applications
    • Mu, J. C. et al. VarSim: a high-fidelity simulation and validation framework for high-throughput genome sequencing with cancer applications. Bioinformatics 31, 1469-1471 (2014).
    • (2014) Bioinformatics , vol.31 , pp. 1469-1471
    • Mu, J.C.1
  • 30
    • 84858433310 scopus 로고    scopus 로고
    • Personal omics profiling reveals dynamic molecular and medical phenotypes
    • Chen, R. et al. Personal omics profiling reveals dynamic molecular and medical phenotypes. Cell 148, 1293-1307 (2012).
    • (2012) Cell , vol.148 , pp. 1293-1307
    • Chen, R.1
  • 31
    • 63849094762 scopus 로고    scopus 로고
    • HapMap methylation-associated SNPs, markers of germline DNA methylation, positively correlate with regional levels of human meiotic recombination
    • Sigurdsson, M. I., Smith, A. V., Bjornsson, H. T. & Jonsson, J. J. HapMap methylation-associated SNPs, markers of germline DNA methylation, positively correlate with regional levels of human meiotic recombination. Genome Res. 19, 581-589 (2009).
    • (2009) Genome Res. , vol.19 , pp. 581-589
    • Sigurdsson, M.I.1    Smith, A.V.2    Bjornsson, H.T.3    Jonsson, J.J.4
  • 32
    • 1842717957 scopus 로고    scopus 로고
    • Comparative recombination rates in the rat, mouse, and human genomes
    • Jensen-Seaman, M. I. et al. Comparative recombination rates in the rat, mouse, and human genomes. Genome Res. 14, 528-538 (2004).
    • (2004) Genome Res. , vol.14 , pp. 528-538
    • Jensen-Seaman, M.I.1
  • 33
    • 80052937538 scopus 로고    scopus 로고
    • Sperm methylation profiles reveal features of epigenetic inheritance and evolution in primates
    • Molaro, A. et al. Sperm methylation profiles reveal features of epigenetic inheritance and evolution in primates. Cell 146, 1029-1041 (2011).
    • (2011) Cell , vol.146 , pp. 1029-1041
    • Molaro, A.1
  • 34
    • 0028575909 scopus 로고
    • Alu repeated DNAs are differentially methylated in primate germ cells
    • Rubin, C. M., VandeVoort, C. A., Teplitz, R. L. & Schmid, C. W. Alu repeated DNAs are differentially methylated in primate germ cells. Nucleic Acids Res. 22, 5121-5127 (1994).
    • (1994) Nucleic Acids Res. , vol.22 , pp. 5121-5127
    • Rubin, C.M.1    Vandevoort, C.A.2    Teplitz, R.L.3    Schmid, C.W.4
  • 35
    • 84865285978 scopus 로고    scopus 로고
    • Landscape of somatic retrotransposition in human cancers
    • Lee, E. et al. Landscape of somatic retrotransposition in human cancers. Science 337, 967-971 (2012).
    • (2012) Science , vol.337 , pp. 967-971
    • Lee, E.1
  • 36
    • 70349873824 scopus 로고    scopus 로고
    • Comprehensive mapping of long-range interactions reveals folding principles of the human genome
    • Lieberman-Aiden, E. et al. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 326, 289-293 (2009).
    • (2009) Science , vol.326 , pp. 289-293
    • Lieberman-Aiden, E.1
  • 37
    • 85027936863 scopus 로고    scopus 로고
    • Replicative mechanisms for CNV formation are error prone
    • Carvalho, C. M. B. et al. Replicative mechanisms for CNV formation are error prone. Nat. Genet. 45, 1319-1326 (2013).
    • (2013) Nat. Genet. , vol.45 , pp. 1319-1326
    • Carvalho, C.M.B.1
  • 38
    • 84870955253 scopus 로고    scopus 로고
    • Differential relationship of DNA replication timing to different forms of human mutation and variation
    • Koren, A. et al. Differential relationship of DNA replication timing to different forms of human mutation and variation. Am. J. Hum. Genet. 91, 1033-1040 (2012).
    • (2012) Am. J. Hum. Genet. , vol.91 , pp. 1033-1040
    • Koren, A.1
  • 39
    • 84888018217 scopus 로고    scopus 로고
    • Organization of the mitotic chromosome
    • Naumova, N. et al. Organization of the mitotic chromosome. Science 342, 948-953 (2013).
    • (2013) Science , vol.342 , pp. 948-953
    • Naumova, N.1
  • 40
    • 84865681429 scopus 로고    scopus 로고
    • TrxG and PcG proteins but not methylated histones remain associated with DNA through replication
    • Petruk, S. et al. TrxG and PcG proteins but not methylated histones remain associated with DNA through replication. Cell 150, 922-933 (2012).
    • (2012) Cell , vol.150 , pp. 922-933
    • Petruk, S.1
  • 41
    • 84863661788 scopus 로고    scopus 로고
    • Genomic hypomethylation in the human germline associates with selective structural mutability in the human genome
    • Li, J. et al. Genomic hypomethylation in the human germline associates with selective structural mutability in the human genome. PLoS Genet. 8, e1002692 (2012).
    • (2012) PLoS Genet. , vol.8
    • Li, J.1
  • 42
    • 84874765261 scopus 로고    scopus 로고
    • Comment on "genomic hypomethylation in the human germline associates with selective structural mutability in the human genome"
    • Watson, C. T., Garg, P. & Sharp, A. J. Comment on "genomic hypomethylation in the human germline associates with selective structural mutability in the human genome". PLoS Genet. 9, e1003332 (2013).
    • (2013) PLoS Genet. , vol.9
    • Watson, C.T.1    Garg, P.2    Sharp, A.J.3
  • 43
    • 67849121611 scopus 로고    scopus 로고
    • Extrachromosomal circular DNA in eukaryotes: Possible involvement in the plasticity of tandem repeats
    • Cohen, S. & Segal, D. Extrachromosomal circular DNA in eukaryotes: possible involvement in the plasticity of tandem repeats. Cytogenet. Genome Res. 124, 327-338 (2009).
    • (2009) Cytogenet. Genome Res. , vol.124 , pp. 327-338
    • Cohen, S.1    Segal, D.2
  • 44
    • 37549018501 scopus 로고    scopus 로고
    • Germline rates of de novo meiotic deletions and duplications causing several genomic disorders
    • Turner, D. J. et al. Germline rates of de novo meiotic deletions and duplications causing several genomic disorders. Nat. Genet. 40, 90-95 (2008).
    • (2008) Nat. Genet. , vol.40 , pp. 90-95
    • Turner, D.J.1
  • 45
    • 84859516414 scopus 로고    scopus 로고
    • Extrachromosomal microDNAs and chromosomal microdeletions in normal tissues
    • Shibata, Y. et al. Extrachromosomal microDNAs and chromosomal microdeletions in normal tissues. Science 336, 82-86 (2012).
    • (2012) Science , vol.336 , pp. 82-86
    • Shibata, Y.1
  • 46
    • 84866997011 scopus 로고    scopus 로고
    • Iterative correction of Hi-C data reveals hallmarks of chromosome organization
    • Imakaev, M. et al. Iterative correction of Hi-C data reveals hallmarks of chromosome organization. Nat. Methods 9, 999-1003 (2012).
    • (2012) Nat. Methods , vol.9 , pp. 999-1003
    • Imakaev, M.1
  • 47
    • 0035863793 scopus 로고    scopus 로고
    • Target DNA chromatinization modulates nicking by L1 endonuclease
    • Cost, G. J., Golding, A., Schlissel, M. S. & Boeke, J. D. Target DNA chromatinization modulates nicking by L1 endonuclease. Nucleic Acids Res. 29, 573-577 (2001).
    • (2001) Nucleic Acids Res. , vol.29 , pp. 573-577
    • Cost, G.J.1    Golding, A.2    Schlissel, M.S.3    Boeke, J.D.4
  • 48
    • 79951970227 scopus 로고    scopus 로고
    • CNVnator: An approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing
    • Abyzov, A., Urban, A. E., Snyder, M. & Gerstein, M. CNVnator: an approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing. Genome Res. 21, 974-984 (2011).
    • (2011) Genome Res. , vol.21 , pp. 974-984
    • Abyzov, A.1    Urban, A.E.2    Snyder, M.3    Gerstein, M.4
  • 49
    • 84866440781 scopus 로고    scopus 로고
    • DELLY: Structural variant discovery by integrated paired-end and split-read analysis
    • Rausch, T. et al. DELLY: structural variant discovery by integrated paired-end and split-read analysis. Bioinformatics 28, i333-i339 (2012).
    • (2012) Bioinformatics , vol.28 , pp. i333-i339
    • Rausch, T.1
  • 50
    • 79952194317 scopus 로고    scopus 로고
    • Discovery and genotyping of genome structural polymorphism by sequencing on a population scale
    • Handsaker, R. E., Korn, J. M., Nemesh, J. & McCarroll, S. A. Discovery and genotyping of genome structural polymorphism by sequencing on a population scale. Nat. Genet. 43, 269-276 (2011).
    • (2011) Nat. Genet. , vol.43 , pp. 269-276
    • Handsaker, R.E.1    Korn, J.M.2    Nemesh, J.3    McCarroll, S.A.4
  • 51
    • 70350694443 scopus 로고    scopus 로고
    • Pindel: A pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads
    • Ye, K., Schulz, M., Long, Q., Apweiler, R. & Ning, Z. Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads. Bioinformatics 25, 2865-2871 (2009).
    • (2009) Bioinformatics , vol.25 , pp. 2865-2871
    • Ye, K.1    Schulz, M.2    Long, Q.3    Apweiler, R.4    Ning, Z.5
  • 52
    • 69549116107 scopus 로고    scopus 로고
    • BreakDancer: An algorithm for high-resolution mapping of genomic structural variation
    • Chen, K. et al. BreakDancer: an algorithm for high-resolution mapping of genomic structural variation. Nat. Methods 6, 677-681 (2009).
    • (2009) Nat. Methods , vol.6 , pp. 677-681
    • Chen, K.1
  • 53
    • 4944262040 scopus 로고    scopus 로고
    • Glocal alignment: Finding rearrangements during alignment
    • Brudno, M. et al. Glocal alignment: finding rearrangements during alignment. Bioinformatics 19(Suppl 1): i54-i62 (2003).
    • (2003) Bioinformatics , vol.19 , pp. i54-i62
    • Brudno, M.1
  • 54
    • 84864143346 scopus 로고    scopus 로고
    • BreakFusion: Targeted assembly-based identification of gene fusions in whole transcriptome paired-end sequencing data
    • Chen, K. et al. BreakFusion: targeted assembly-based identification of gene fusions in whole transcriptome paired-end sequencing data. Bioinformatics 28, 1923-1924 (2012).
    • (2012) Bioinformatics , vol.28 , pp. 1923-1924
    • Chen, K.1
  • 55
    • 62349130698 scopus 로고    scopus 로고
    • Ultrafast and memoryefficient alignment of short DNA sequences to the human genome
    • Langmead, B., Trapnell, C., Pop, M. & Salzberg, S. Ultrafast and memoryefficient alignment of short DNA sequences to the human genome. Genome Biol. 10, R25 (2009).
    • (2009) Genome Biol. , vol.10 , pp. R25
    • Langmead, B.1    Trapnell, C.2    Pop, M.3    Salzberg, S.4
  • 56
    • 77949587649 scopus 로고    scopus 로고
    • Fast and accurate long read alignment with Burrows-Wheeler transform
    • Li, H. & Durbin, R. Fast and accurate long read alignment with Burrows-Wheeler transform. Bioinformatics 26, 589-595 (2010).
    • (2010) Bioinformatics , vol.26 , pp. 589-595
    • Li, H.1    Durbin, R.2
  • 57
    • 0036226603 scopus 로고    scopus 로고
    • BLAT - The BLAST-like alignment tool
    • Kent, W. J. BLAT - the BLAST-like alignment tool. Genome Res. 12, 656-664 (2002).
    • (2002) Genome Res. , vol.12 , pp. 656-664
    • Kent, W.J.1


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