Diverse mechanisms of somatic structural variations in human cancer genomes

Cell

Volumn 153, Issue 4, 2013, Pages 919-929

  Yang, Lixing ^a   Luquette, Lovelace J ^a   Gehlenborg, Nils ^a,c   Xi, Ruibin ^a,d   Haseley, Psalm S ^a,e   Hsieh, Chih Heng ^b   Zhang, Chengsheng ^b   Ren, Xiaojia ^e   Protopopov, Alexei ^f   Chin, Lynda ^f   Kucherlapati, Raju ^b,e   Lee, Charles ^b,g   Park, Peter J ^a,e,h  

^a Harvard Medical School Center for Biomedical Informatics   (United States)

^b HARVARD MEDICAL SCHOOL   (United States)

^c BROAD INSTITUTE OF MIT AND HARVARD   (United States)

^d PEKING UNIVERSITY   (China)

^e BRIGHAM AND WOMEN S HOSPITAL   (United States)

^f UNIVERSITY OF TEXAS MD ANDERSON CANCER CENTER   (United States)

^g Seoul National University College of Medicine   (South Korea)

^h BOSTON CHILDREN S HOSPITAL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ARTICLE; CANCER GENETICS; CDKN2A GENE; CDKN2B GENE; DOUBLE STRANDED DNA BREAK; EGFR GENE; GAIN OF FUNCTION MUTATION; GENE; GENE DELETION; GENE MUTATION; GENE REARRANGEMENT; GENE REPLICATION; GENE SEQUENCE; GENE STRUCTURE; GENETIC VARIABILITY; GERM LINE; GLIOBLASTOMA; HUMAN; HUMAN GENOME; LOSS OF FUNCTION MUTATION; MOLECULAR PATHOLOGY; PRIORITY JOURNAL; TUMOR GENE;

EID: 84877722178     PISSN: 00928674     EISSN: 10974172     Source Type: Journal    
DOI: 10.1016/j.cell.2013.04.010     Document Type: Article

References (58)

1. M.F. Arlt, S. Rajendran, S.R. Birkeland, T.E. Wilson, and T.W. Glover De novo CNV formation in mouse embryonic stem cells occurs in the absence of Xrcc4-dependent nonhomologous end joining PLoS Genet. 8 2012 e1002981
2. S. Banerji, K. Cibulskis, C. Rangel-Escareno, K.K. Brown, S.L. Carter, A.M. Frederick, M.S. Lawrence, A.Y. Sivachenko, C. Sougnez, and L. Zou Sequence analysis of mutations and translocations across breast cancer subtypes Nature 486 2012 405 409
3. A.J. Bass, M.S. Lawrence, L.E. Brace, A.H. Ramos, Y. Drier, K. Cibulskis, C. Sougnez, D. Voet, G. Saksena, and A. Sivachenko Genomic sequencing of colorectal adenocarcinomas identifies a recurrent VTI1A-TCF7L2 fusion Nat. Genet. 43 2011 964 968
4. N. Bennardo, A. Cheng, N. Huang, and J.M. Stark Alternative-NHEJ is a mechanistically distinct pathway of mammalian chromosome break repair PLoS Genet. 4 2008 e1000110
5. M.F. Berger, M.S. Lawrence, F. Demichelis, Y. Drier, K. Cibulskis, A.Y. Sivachenko, A. Sboner, R. Esgueva, D. Pflueger, and C. Sougnez The genomic complexity of primary human prostate cancer Nature 470 2011 214 220
6. P.J. Campbell, S. Yachida, L.J. Mudie, P.J. Stephens, E.D. Pleasance, L.A. Stebbings, L.A. Morsberger, C. Latimer, S. McLaren, and M.-L. Lin The patterns and dynamics of genomic instability in metastatic pancreatic cancer Nature 467 2010 1109 1113
7. Cancer Genome Atlas Research Network Comprehensive genomic characterization defines human glioblastoma genes and core pathways Nature 455 2008 1061 1068
8. Cancer Genome Atlas Research Network Comprehensive molecular portraits of human breast tumours Nature 490 2012 61 70
9. Cancer Genome Atlas Research Network Comprehensive genomic characterization of squamous cell lung cancers Nature 489 2012 519 525
10. M.A. Chapman, M.S. Lawrence, J.J. Keats, K. Cibulskis, C. Sougnez, A.C. Schinzel, C.L. Harview, J.-P. Brunet, G.J. Ahmann, and M. Adli Initial genome sequencing and analysis of multiple myeloma Nature 471 2011 467 472
11. C. Chiang, J.C. Jacobsen, C. Ernst, C. Hanscom, A. Heilbut, I. Blumenthal, R.E. Mills, A. Kirby, A.M. Lindgren, and S.R. Rudiger Complex reorganization and predominant non-homologous repair following chromosomal breakage in karyotypically balanced germline rearrangements and transgenic integration Nat. Genet. 44 2012 390 397 S1
12. D.F. Conrad, C. Bird, B. Blackburne, S. Lindsay, L. Mamanova, C. Lee, D.J. Turner, and M.E. Hurles Mutation spectrum revealed by breakpoint sequencing of human germline CNVs Nat. Genet. 42 2010 385 391
13. S. De, and F. Michor DNA replication timing and long-range DNA interactions predict mutational landscapes of cancer genomes Nat. Biotechnol. 29 2011 1103 1108
14. S. De, and F. Michor DNA secondary structures and epigenetic determinants of cancer genome evolution Nat. Struct. Mol. Biol. 18 2011 950 955
15. I. Dunham, A. Kundaje, S.F. Aldred, P.J. Collins, C.A. Davis, F. Doyle, C.B. Epstein, S. Frietze, J. Harrow, R. Kaul ENCODE Project Consortium An integrated encyclopedia of DNA elements in the human genome Nature 489 2012 57 74
16. T. Edlund, and S. Normark Recombination between short DNA homologies causes tandem duplication Nature 292 1981 269 271
17. G. Fudenberg, G. Getz, M. Meyerson, and L.A. Mirny High order chromatin architecture shapes the landscape of chromosomal alterations in cancer Nat. Biotechnol. 29 2011 1109 1113
18. C. Greenman, P. Stephens, R. Smith, G.L. Dalgliesh, C. Hunter, G. Bignell, H. Davies, J. Teague, A. Butler, and C. Stevens Patterns of somatic mutation in human cancer genomes Nature 446 2007 153 158
19. W. Gu, F. Zhang, and J.R. Lupski Mechanisms for human genomic rearrangements Pathogenetics 1 2008 4
20. M.C. Haffner, M.J. Aryee, A. Toubaji, D.M. Esopi, R. Albadine, B. Gurel, W.B. Isaacs, G.S. Bova, W. Liu, and J. Xu Androgen-induced TOP2B-mediated double-strand breaks and prostate cancer gene rearrangements Nat. Genet. 42 2010 668 675
21. P.J. Hastings, G. Ira, and J.R. Lupski A microhomology-mediated break-induced replication model for the origin of human copy number variation PLoS Genet. 5 2009 e1000327
22. P.J. Hastings, J.R. Lupski, S.M. Rosenberg, and G. Ira Mechanisms of change in gene copy number Nat. Rev. Genet. 10 2009 551 564
23. A. Haviv-Chesner, Y. Kobayashi, A. Gabriel, and M. Kupiec Capture of linear fragments at a double-strand break in yeast Nucleic Acids Res. 35 2007 5192 5202
24. A.M. Hillmer, F. Yao, K. Inaki, W.H. Lee, P.N. Ariyaratne, A.S.M. Teo, X.Y. Woo, Z. Zhang, H. Zhao, and L. Ukil Comprehensive long-span paired-end-tag mapping reveals characteristic patterns of structural variations in epithelial cancer genomes Genome Res. 21 2011 665 675
25. J.H.J. Hoeijmakers Genome maintenance mechanisms for preventing cancer Nature 411 2001 366 374
26. A.J. Iafrate, L. Feuk, M.N. Rivera, M.L. Listewnik, P.K. Donahoe, Y. Qi, S.W. Scherer, and C. Lee Detection of large-scale variation in the human genome Nat. Genet. 36 2004 949 951
27. J.M. Kidd, T. Graves, T.L. Newman, R. Fulton, H.S. Hayden, M. Malig, J. Kallicki, R. Kaul, R.K. Wilson, and E.E. Eichler A human genome structural variation sequencing resource reveals insights into mutational mechanisms Cell 143 2010 837 847
28. H.Y.K. Lam, X.J. Mu, A.M. Stütz, A. Tanzer, P.D. Cayting, M. Snyder, P.M. Kim, J.O. Korbel, and M.B. Gerstein Nucleotide-resolution analysis of structural variants using BreakSeq and a breakpoint library Nat. Biotechnol. 28 2010 47 55
29. J.A. Lee, C.M. Carvalho, and J.R. Lupski A DNA replication mechanism for generating nonrecurrent rearrangements associated with genomic disorders Cell 131 2007 1235 1247
30. W. Lee, Z. Jiang, J. Liu, P.M. Haverty, Y. Guan, J. Stinson, P. Yue, Y. Zhang, K.P. Pant, and D. Bhatt The mutation spectrum revealed by paired genome sequences from a lung cancer patient Nature 465 2010 473 477
31. E. Lee, R. Iskow, L. Yang, O. Gokcumen, P. Haseley, L.J. Luquette 3rd, J.G. Lohr, C.C. Harris, L. Ding, R.K. Wilson Cancer Genome Atlas Research Network Landscape of somatic retrotransposition in human cancers Science 337 2012 967 971
32. R.M. Liskay, A. Letsou, and J.L. Stachelek Homology requirement for efficient gene conversion between duplicated chromosomal sequences in mammalian cells Genetics 115 1987 161 167
33. P. Liu, A. Erez, S.C. Nagamani, S.U. Dhar, K.E. Kołodziejska, A.V. Dharmadhikari, M.L. Cooper, J. Wiszniewska, F. Zhang, and M.A. Withers Chromosome catastrophes involve replication mechanisms generating complex genomic rearrangements Cell 146 2011 889 903
34. B.L. Mahaney, K. Meek, and S.P. Lees-Miller Repair of ionizing radiation-induced DNA double-strand breaks by non-homologous end-joining Biochem. J. 417 2009 639 650
35. M. McVey, and S.E. Lee MMEJ repair of double-strand breaks (director's cut): deleted sequences and alternative endings Trends Genet. 24 2008 529 538
36. R.E. Mills, K. Walter, C. Stewart, R.E. Handsaker, K. Chen, C. Alkan, A. Abyzov, S.C. Yoon, K. Ye, R.K. Cheetham 1000 Genomes Project Mapping copy number variation by population-scale genome sequencing Nature 470 2011 59 65
37. E.D. Pleasance, R.K. Cheetham, P.J. Stephens, D.J. McBride, S.J. Humphray, C.D. Greenman, I. Varela, M.-L. Lin, G.R. Ordóñez, and G.R. Bignell A comprehensive catalogue of somatic mutations from a human cancer genome Nature 463 2010 191 196
38. E.D. Pleasance, P.J. Stephens, S. O'Meara, D.J. McBride, A. Meynert, D. Jones, M.-L. Lin, D. Beare, K.W. Lau, and C. Greenman A small-cell lung cancer genome with complex signatures of tobacco exposure Nature 463 2010 184 190
39. D.A. Solomon, T. Kim, L.A. Diaz-Martinez, J. Fair, A.G. Elkahloun, B.T. Harris, J.A. Toretsky, S.A. Rosenberg, N. Shukla, and M. Ladanyi Mutational inactivation of STAG2 causes aneuploidy in human cancer Science 333 2011 1039 1043
40. P.J. Stephens, D.J. McBride, M.-L. Lin, I. Varela, E.D. Pleasance, J.T. Simpson, L.A. Stebbings, C. Leroy, S. Edkins, and L.J. Mudie Complex landscapes of somatic rearrangement in human breast cancer genomes Nature 462 2009 1005 1010
41. P.J. Stephens, C.D. Greenman, B. Fu, F. Yang, G.R. Bignell, L.J. Mudie, E.D. Pleasance, K.W. Lau, D. Beare, and L.A. Stebbings Massive genomic rearrangement acquired in a single catastrophic event during cancer development Cell 144 2011 27 40
42. C.T. Storlazzi, A. Lonoce, M.C. Guastadisegni, D. Trombetta, P. D'Addabbo, G. Daniele, A. L'Abbate, G. Macchia, C. Surace, and K. Kok Gene amplification as double minutes or homogeneously staining regions in solid tumors: origin and structure Genome Res. 20 2010 1198 1206
43. W.K. Sung, H. Zheng, S. Li, R. Chen, X. Liu, Y. Li, N.P. Lee, W.H. Lee, P.N. Ariyaratne, and C. Tennakoon Genome-wide survey of recurrent HBV integration in hepatocellular carcinoma Nat. Genet. 44 2012 765 769
44. L. Thomas, J. Stamberg, I. Gojo, Y. Ning, and A.P. Rapoport Double minute chromosomes in monoblastic (M5) and myeloblastic (M2) acute myeloid leukemia: two case reports and a review of literature Am. J. Hematol. 77 2004 55 61
45. N. Van Roy, J. Vandesompele, B. Menten, H. Nilsson, E. De Smet, M. Rocchi, A. De Paepe, S. Påhlman, and F. Speleman Translocation-excision- deletion-amplification mechanism leading to nonsyntenic coamplification of MYC and ATBF1 Genes Chromosomes Cancer 45 2006 107 117
46. A.R. Venkitaraman Cancer susceptibility and the functions of BRCA1 and BRCA2 Cell 108 2002 171 182
47. N. Vogt, S.H. Lefèvre, F. Apiou, A.M. Dutrillaux, A. Cör, P. Leuraud, M.F. Poupon, B. Dutrillaux, M. Debatisse, and B. Malfoy Molecular structure of double-minute chromosomes bearing amplified copies of the epidermal growth factor receptor gene in gliomas Proc. Natl. Acad. Sci. USA 101 2004 11368 11373
48. A.S. Waldman, and R.M. Liskay Dependence of intrachromosomal recombination in mammalian cells on uninterrupted homology Mol. Cell. Biol. 8 1988 5350 5357
49. F. Zhang, M. Khajavi, A.M. Connolly, C.F. Towne, S.D. Batish, and J.R. Lupski The DNA replication FoSTeS/MMBIR mechanism can generate genomic, genic and exonic complex rearrangements in humans Nat. Genet. 41 2009 849 853
50. K. Chen, J.W. Wallis, M.D. McLellan, D.E. Larson, J.M. Kalicki, C.S. Pohl, S.D. McGrath, M.C. Wendl, Q. Zhang, and D.P. Locke BreakDancer: an algorithm for high-resolution mapping of genomic structural variation Nat. Methods 6 2009 677 681
51. P.J. Gardina, K.C. Lo, W. Lee, J.K. Cowell, and Y. Turpaz Ploidy status and copy number aberrations in primary glioblastomas defined by integrated analysis of allelic ratios, signal ratios and loss of heterozygosity using 500K SNP Mapping Arrays BMC Genomics 9 2008 489
52. F. Hormozdiari, C. Alkan, E.E. Eichler, and S.C. Sahinalp Combinatorial algorithms for structural variation detection in high-throughput sequenced genomes Genome Res. 19 2009 1270 1278
53. H. Li, and R. Durbin Fast and accurate short read alignment with Burrows-Wheeler transform Bioinformatics 25 2009 1754 1760
54. H. Li, B. Handsaker, A. Wysoker, T. Fennell, J. Ruan, N. Homer, G. Marth, G. Abecasis, R. Durbin 1000 Genome Project Data Processing Subgroup The sequence alignment/map format and SAMtools Bioinformatics 25 2009 2078 2079
55. G.H. Perry, A. Ben-Dor, A. Tsalenko, N. Sampas, L. Rodriguez-Revenga, C.W. Tran, A. Scheffer, I. Steinfeld, P. Tsang, and N.A. Yamada The fine-scale and complex architecture of human copy-number variation Am. J. Hum. Genet. 82 2008 685 695
56. A.R. Quinlan, R.A. Clark, S. Sokolova, M.L. Leibowitz, Y. Zhang, M.E. Hurles, J.C. Mell, and I.M. Hall Genome-wide mapping and assembly of structural variant breakpoints in the mouse genome Genome Res. 20 2010 623 635
57. J. Wang, C.G. Mullighan, J. Easton, S. Roberts, S.L. Heatley, J. Ma, M.C. Rusch, K. Chen, C.C. Harris, and L. Ding CREST maps somatic structural variation in cancer genomes with base-pair resolution Nat. Methods 8 2011 652 654
58. R. Xi, A.G. Hadjipanayis, L.J. Luquette, T.M. Kim, E. Lee, J. Zhang, M.D. Johnson, D.M. Muzny, D.A. Wheeler, and R.A. Gibbs Copy number variation detection in whole-genome sequencing data using the Bayesian information criterion Proc. Natl. Acad. Sci. USA 108 2011 E1128 E1136