Next-generation sequencing of duplication CNVs reveals that most are tandem and some create fusion genes at breakpoints

American Journal of Human Genetics

Volumn 96, Issue 2, 2015, Pages 208-220

  Newman, Scott ^a   Hermetz, Karen E ^a   Weckselblatt, Brooke ^a   Rudd, M Katharine ^a  

^a EMORY UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; COPY NUMBER VARIATION; CYTOGENETICS; FUSION GENE; GENE DUPLICATION; GENE FUSION; GENE REARRANGEMENT; HUMAN; NEXT GENERATION SEQUENCING; PHENOTYPE; PRIORITY JOURNAL; SEQUENCE ANALYSIS; WHOLE GENOME SEQUENCING; CHROMOSOMAL MAPPING; CHROMOSOME BREAKAGE; COMPARATIVE GENOMIC HYBRIDIZATION; GENETICS; GENOMICS; HIGH THROUGHPUT SEQUENCING; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PROCEDURES;

BASE SEQUENCE; CHROMOSOME BREAKPOINTS; CHROMOSOME MAPPING; COMPARATIVE GENOMIC HYBRIDIZATION; DNA COPY NUMBER VARIATIONS; GENE DUPLICATION; GENE FUSION; GENOMICS; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; MOLECULAR SEQUENCE DATA;

EID: 84925096537     PISSN: 00029297     EISSN: 15376605     Source Type: Journal    
DOI: 10.1016/j.ajhg.2014.12.017     Document Type: Article

References (69)

1. N.J. Neill, B.S. Torchia, B.A. Bejjani, L.G. Shaffer, and B.C. Ballif Comparative analysis of copy number detection by whole-genome BAC and oligonucleotide array CGH Mol. Cytogenet. 3 2010 11
2. G.M. Cooper, B.P. Coe, S. Girirajan, J.A. Rosenfeld, T.H. Vu, C. Baker, C. Williams, H. Stalker, R. Hamid, and V. Hannig A copy number variation morbidity map of developmental delay Nat. Genet. 43 2011 838 846
3. H.M. Kearney, E.C. Thorland, K.K. Brown, F. Quintero-Rivera, S.T. South Working Group of the American College of Medical Genetics Laboratory Quality Assurance Committee American College of Medical Genetics standards and guidelines for interpretation and reporting of postnatal constitutional copy number variants Genet. Med. 13 2011 680 685
4. C.T. Watson, T. Marques-Bonet, A.J. Sharp, and H.C. Mefford The genetics of microdeletion and microduplication syndromes: an update Annu. Rev. Genomics Hum. Genet. 15 2014 215 244
5. E.H. Cook Jr., and S.W. Scherer Copy-number variations associated with neuropsychiatric conditions Nature 455 2008 919 923
6. K.L. Deak, S.R. Horn, and C.W. Rehder The evolving picture of microdeletion/microduplication syndromes in the age of microarray analysis: variable expressivity and genomic complexity Clin. Lab. Med. 31 2011 543 564 viii
7. J.A. Rosenfeld, B.P. Coe, E.E. Eichler, H. Cuckle, and L.G. Shaffer Estimates of penetrance for recurrent pathogenic copy-number variations Genet. Med. 15 2013 478 481
8. A. Itsara, G.M. Cooper, C. Baker, S. Girirajan, J. Li, D. Absher, R.M. Krauss, R.M. Myers, P.M. Ridker, and D.I. Chasman Population analysis of large copy number variants and hotspots of human genetic disease Am. J. Hum. Genet. 84 2009 148 161
9. M.K. Rudd, J. Keene, B. Bunke, E.B. Kaminsky, M.P. Adam, J.G. Mulle, D.H. Ledbetter, and C.L. Martin Segmental duplications mediate novel, clinically relevant chromosome rearrangements Hum. Mol. Genet. 18 2009 2957 2962
10. 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
11. B. Thienpont, F. Béna, J. Breckpot, N. Philip, B. Menten, H. Van Esch, E. Scalais, J.M. Salamone, C.T. Fong, and J.L. Kussmann Duplications of the critical Rubinstein-Taybi deletion region on chromosome 16p13.3 cause a novel recognisable syndrome J. Med. Genet. 47 2010 155 161
12. E. Giorgio, H. Rolyan, L. Kropp, A.B. Chakka, S. Yatsenko, E. Di Gregorio, D. Lacerenza, G. Vaula, F. Talarico, and P. Mandich Analysis of LMNB1 duplications in autosomal dominant leukodystrophy provides insights into duplication mechanisms and allele-specific expression Hum. Mutat. 34 2013 1160 1171
13. H. Van Esch, M. Bauters, J. Ignatius, M. Jansen, M. Raynaud, K. Hollanders, D. Lugtenberg, T. Bienvenu, L.R. Jensen, and J. Gecz Duplication of the MECP2 region is a frequent cause of severe mental retardation and progressive neurological symptoms in males Am. J. Hum. Genet. 77 2005 442 453
14. K.J. Woodward, M. Cundall, K. Sperle, E.A. Sistermans, M. Ross, G. Howell, S.M. Gribble, D.C. Burford, N.P. Carter, and D.L. Hobson Heterogeneous duplications in patients with Pelizaeus-Merzbacher disease suggest a mechanism of coupled homologous and nonhomologous recombination Am. J. Hum. Genet. 77 2005 966 987
15. M.F. Arlt, J.G. Mulle, V.M. Schaibley, R.L. Ragland, S.G. Durkin, S.T. Warren, and T.W. Glover Replication stress induces genome-wide copy number changes in human cells that resemble polymorphic and pathogenic variants Am. J. Hum. Genet. 84 2009 339 350
16. 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
17. 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
18. E.L. Baldwin, J.Y. Lee, D.M. Blake, B.P. Bunke, C.R. Alexander, A.L. Kogan, D.H. Ledbetter, and C.L. Martin Enhanced detection of clinically relevant genomic imbalances using a targeted plus whole genome oligonucleotide microarray Genet. Med. 10 2008 415 429
19. Y. Luo, K.E. Hermetz, J.M. Jackson, J.G. Mulle, A. Dodd, K.D. Tsuchiya, B.C. Ballif, L.G. Shaffer, J.D. Cody, and D.H. Ledbetter Diverse mutational mechanisms cause pathogenic subtelomeric rearrangements Hum. Mol. Genet. 20 2011 3769 3778
20. H. Li, and R. Durbin Fast and accurate short read alignment with Burrows-Wheeler transform Bioinformatics 25 2009 1754 1760
21. 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
22. C.K. Ng, S.L. Cooke, K. Howe, S. Newman, J. Xian, J. Temple, E.M. Batty, J.C. Pole, S.P. Langdon, P.A. Edwards, and J.D. Brenton The role of tandem duplicator phenotype in tumour evolution in high-grade serous ovarian cancer J. Pathol. 226 2012 703 712
23. J.T. Robinson, H. Thorvaldsdóttir, W. Winckler, M. Guttman, E.S. Lander, G. Getz, and J.P. Mesirov Integrative genomics viewer Nat. Biotechnol. 29 2011 24 26
24. R. Drmanac, A.B. Sparks, M.J. Callow, A.L. Halpern, N.L. Burns, B.G. Kermani, P. Carnevali, I. Nazarenko, G.B. Nilsen, and G. Yeung Human genome sequencing using unchained base reads on self-assembling DNA nanoarrays Science 327 2010 78 81
25. A.R. Quinlan, and I.M. Hall BEDTools: a flexible suite of utilities for comparing genomic features Bioinformatics 26 2010 841 842
26. W.J. Kent BLAT - the BLAST-like alignment tool Genome Res. 12 2002 656 664
27. P. Flicek, M.R. Amode, D. Barrell, K. Beal, K. Billis, S. Brent, D. Carvalho-Silva, P. Clapham, G. Coates, and S. Fitzgerald Ensembl 2014 Nucleic Acids Res. 42 2014 D749 D755
28. T.H. Shaikh, X. Gai, J.C. Perin, J.T. Glessner, H. Xie, K. Murphy, R. O'Hara, T. Casalunovo, L.K. Conlin, and M. D'Arcy High-resolution mapping and analysis of copy number variations in the human genome: a data resource for clinical and research applications Genome Res. 19 2009 1682 1690
29. J.R. MacDonald, R. Ziman, R.K. Yuen, L. Feuk, and S.W. Scherer The Database of Genomic Variants: a curated collection of structural variation in the human genome Nucleic Acids Res. 42 2014 D986 D992
30. 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
31. C.M. Carvalho, D. Pehlivan, M.B. Ramocki, P. Fang, B. Alleva, L.M. Franco, J.W. Belmont, P.J. Hastings, and J.R. Lupski Replicative mechanisms for CNV formation are error prone Nat. Genet. 45 2013 1319 1326
32. H. Brand, V. Pillalamarri, R.L. Collins, S. Eggert, C. O'Dushlaine, E.B. Braaten, M.R. Stone, K. Chambert, N.D. Doty, and C. Hanscom Cryptic and complex chromosomal aberrations in early-onset neuropsychiatric disorders Am. J. Hum. Genet. 95 2014 454 461
33. K.E. Hermetz, S. Newman, K.N. Conneely, C.L. Martin, B.C. Ballif, L.G. Shaffer, J.D. Cody, and M.K. Rudd Large inverted duplications in the human genome form via a fold-back mechanism PLoS Genet. 10 2014 e1004139
34. T. Fernandez, T. Morgan, N. Davis, A. Klin, A. Morris, A. Farhi, R.P. Lifton, and M.W. State Disruption of contactin 4 (CNTN4) results in developmental delay and other features of 3p deletion syndrome Am. J. Hum. Genet. 74 2004 1286 1293
35. J. Roohi, C. Montagna, D.H. Tegay, L.E. Palmer, C. DeVincent, J.C. Pomeroy, S.L. Christian, N. Nowak, and E. Hatchwell Disruption of contactin 4 in three subjects with autism spectrum disorder J. Med. Genet. 46 2009 176 182
36. C.E. Cottrell, N. Bir, E. Varga, C.E. Alvarez, S. Bouyain, R. Zernzach, D.L. Thrush, J. Evans, M. Trimarchi, and E.M. Butter Contactin 4 as an autism susceptibility locus Autism Res. 4 2011 189 199
37. M. Tartaglia, L.A. Pennacchio, C. Zhao, K.K. Yadav, V. Fodale, A. Sarkozy, B. Pandit, K. Oishi, S. Martinelli, and W. Schackwitz Gain-of-function SOS1 mutations cause a distinctive form of Noonan syndrome Nat. Genet. 39 2007 75 79
38. M. Zenker, D. Horn, D. Wieczorek, J. Allanson, S. Pauli, I. van der Burgt, H.G. Doerr, H. Gaspar, M. Hofbeck, and G. Gillessen-Kaesbach SOS1 is the second most common Noonan gene but plays no major role in cardio-facio-cutaneous syndrome J. Med. Genet. 44 2007 651 656
39. K.R. Veeramah, L. Johnstone, T.M. Karafet, D. Wolf, R. Sprissler, J. Salogiannis, A. Barth-Maron, M.E. Greenberg, T. Stuhlmann, and S. Weinert Exome sequencing reveals new causal mutations in children with epileptic encephalopathies Epilepsia 54 2013 1270 1281
40. R. Redon, S. Ishikawa, K.R. Fitch, L. Feuk, G.H. Perry, T.D. Andrews, H. Fiegler, M.H. Shapero, A.R. Carson, and W. Chen Global variation in copy number in the human genome Nature 444 2006 444 454
41. A.K. Arndt, S. Schafer, J.D. Drenckhahn, M.K. Sabeh, E.R. Plovie, A. Caliebe, E. Klopocki, G. Musso, A.A. Werdich, and H. Kalwa Fine mapping of the 1p36 deletion syndrome identifies mutation of PRDM16 as a cause of cardiomyopathy Am. J. Hum. Genet. 93 2013 67 77
42. R. Soemedi, I.J. Wilson, J. Bentham, R. Darlay, A. Töpf, D. Zelenika, C. Cosgrove, K. Setchfield, C. Thornborough, and J. Granados-Riveron Contribution of global rare copy-number variants to the risk of sporadic congenital heart disease Am. J. Hum. Genet. 91 2012 489 501
43. D. Warburton, M. Ronemus, J. Kline, V. Jobanputra, I. Williams, K. Anyane-Yeboa, W. Chung, L. Yu, N. Wong, and D. Awad The contribution of de novo and rare inherited copy number changes to congenital heart disease in an unselected sample of children with conotruncal defects or hypoplastic left heart disease Hum. Genet. 133 2014 11 27
44. C.M. Carvalho, M.B. Ramocki, D. Pehlivan, L.M. Franco, C. Gonzaga-Jauregui, P. Fang, A. McCall, E.K. Pivnick, S. Hines-Dowell, and L.H. Seaver Inverted genomic segments and complex triplication rearrangements are mediated by inverted repeats in the human genome Nat. Genet. 43 2011 1074 1081
45. R. Giorda, S. Beri, M.C. Bonaglia, L. Spaccini, B. Scelsa, E. Manolakos, E. Della Mina, R. Ciccone, and O. Zuffardi Common structural features characterize interstitial intrachromosomal Xp and 18q triplications Am. J. Med. Genet. A. 155A 2011 2681 2687
46. K. Shimojima, T. Mano, M. Kashiwagi, T. Tanabe, M. Sugawara, N. Okamoto, H. Arai, and T. Yamamoto Pelizaeus-Merzbacher disease caused by a duplication-inverted triplication-duplication in chromosomal segments including the PLP1 region Eur. J. Med. Genet. 55 2012 400 403
47. A. Fujita, H. Suzumura, M. Nakashima, Y. Tsurusaki, H. Saitsu, N. Harada, N. Matsumoto, and N. Miyake A unique case of de novo 5q33.3-q34 triplication with uniparental isodisomy of 5q34-qter Am. J. Med. Genet. A. 161A 2013 1904 1909
48. C. Soler-Alfonso, C.M. Carvalho, J. Ge, E.K. Roney, P.I. Bader, K.E. Kolodziejska, R.M. Miller, J.R. Lupski, P. Stankiewicz, and S.W. Cheung CHRNA7 triplication associated with cognitive impairment and neuropsychiatric phenotypes in a three-generation pedigree Eur. J. Hum. Genet. 22 2014 1071 1076
49. P. Liu, C.M. Carvalho, P.J. Hastings, and J.R. Lupski Mechanisms for recurrent and complex human genomic rearrangements Curr. Opin. Genet. Dev. 22 2012 211 220
50. S.H. Kang, C. Shaw, Z. Ou, P.A. Eng, M.L. Cooper, A.N. Pursley, T. Sahoo, C.A. Bacino, A.C. Chinault, and P. Stankiewicz Insertional translocation detected using FISH confirmation of array-comparative genomic hybridization (aCGH) results Am. J. Med. Genet. A. 152A 2010 1111 1126
51. N.J. Neill, B.C. Ballif, A.N. Lamb, S. Parikh, J.B. Ravnan, R.A. Schultz, B.S. Torchia, J.A. Rosenfeld, and L.G. Shaffer Recurrence, submicroscopic complexity, and potential clinical relevance of copy gains detected by array CGH that are shown to be unbalanced insertions by FISH Genome Res. 21 2011 535 544
52. B.A. Nowakowska, N. de Leeuw, C.A. Ruivenkamp, B. Sikkema-Raddatz, J.A. Crolla, R. Thoelen, M. Koopmans, N. den Hollander, A. van Haeringen, and A.M. van der Kevie-Kersemaekers Parental insertional balanced translocations are an important cause of apparently de novo CNVs in patients with developmental anomalies Eur. J. Hum. Genet. 20 2012 166 170
53. G. Lev-Maor, O. Ram, E. Kim, N. Sela, A. Goren, E.Y. Levanon, and G. Ast Intronic Alus influence alternative splicing PLoS Genet. 4 2008 e1000204
54. U. Hellsten, J.L. Aspden, D.C. Rio, and D.S. Rokhsar A segmental genomic duplication generates a functional intron Nat. Commun. 2 2011 454
55. S. Medves, and J.B. Demoulin Tyrosine kinase gene fusions in cancer: translating mechanisms into targeted therapies J. Cell. Mol. Med. 16 2012 237 248
56. 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
57. C.M. Carvalho, F. Zhang, P. Liu, A. Patel, T. Sahoo, C.A. Bacino, C. Shaw, S. Peacock, A. Pursley, and Y.J. Tavyev Complex rearrangements in patients with duplications of MECP2 can occur by fork stalling and template switching Hum. Mol. Genet. 18 2009 2188 2203
58. G. Froyen, S. Belet, F. Martinez, C.B. Santos-Rebouças, M. Declercq, J. Verbeeck, L. Donckers, S. Berland, S. Mayo, and M. Rosello Copy-number gains of HUWE1 due to replication- and recombination-based rearrangements Am. J. Hum. Genet. 91 2012 252 264
59. R. Giorda, M.C. Bonaglia, S. Beri, M. Fichera, F. Novara, P. Magini, J. Urquhart, F.H. Sharkey, C. Zucca, and R. Grasso Complex segmental duplications mediate a recurrent dup(X)(p11.22-p11.23) associated with mental retardation, speech delay, and EEG anomalies in males and females Am. J. Hum. Genet. 85 2009 394 400
60. P. Bose, K.E. Hermetz, K.N. Conneely, and M.K. Rudd Tandem repeats and G-rich sequences are enriched at human CNV breakpoints PLoS ONE 9 2014 e101607
61. P.M. Boone, B. Yuan, I.M. Campbell, J.C. Scull, M.A. Withers, B.C. Baggett, C.R. Beck, C.J. Shaw, P. Stankiewicz, and P. Moretti The Alu-rich genomic architecture of SPAST predisposes to diverse and functionally distinct disease-associated CNV alleles Am. J. Hum. Genet. 95 2014 143 161
62. E.B. Kaminsky, V. Kaul, J. Paschall, D.M. Church, B. Bunke, D. Kunig, D. Moreno-De-Luca, A. Moreno-De-Luca, J.G. Mulle, and S.T. Warren An evidence-based approach to establish the functional and clinical significance of copy number variants in intellectual and developmental disabilities Genet. Med. 13 2011 777 784
63. M.K. Rudd Structural variation in subtelomeres L. Feuk, Genomic Structural Variants: Methods and Protocols 2011 Springer Science+Business Media New York
64. 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
65. J.J. Michaelson, and J. Sebat forestSV: structural variant discovery through statistical learning Nat. Methods 9 2012 819 821
66. N. Krumm, P.H. Sudmant, A. Ko, B.J. O'Roak, M. Malig, B.P. Coe, A.R. Quinlan, D.A. Nickerson, E.E. Eichler NHLBI Exome Sequencing Project Copy number variation detection and genotyping from exome sequence data Genome Res. 22 2012 1525 1532
67. M. Fromer, J.L. Moran, K. Chambert, E. Banks, S.E. Bergen, D.M. Ruderfer, R.E. Handsaker, S.A. McCarroll, M.C. O'Donovan, and M.J. Owen Discovery and statistical genotyping of copy-number variation from whole-exome sequencing depth Am. J. Hum. Genet. 91 2012 597 607
68. C.S. Poultney, A.P. Goldberg, E. Drapeau, Y. Kou, H. Harony-Nicolas, Y. Kajiwara, S. De Rubeis, S. Durand, C. Stevens, and K. Rehnström Identification of small exonic CNV from whole-exome sequence data and application to autism spectrum disorder Am. J. Hum. Genet. 93 2013 607 619
69. M. Fromer, and S.M. Purcell Using XHMM software to detect copy number variation in whole-exome sequencing data Curr. Protoc. Hum. Genet. 81 2014 1, 21