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  1. LETTER: Analysis of copy number variants and segmental duplications in the human genome: Evidence for a change in the process of formation in recent evolutionary history
    • Philip M. Kim,
    • Hugo Y.K. Lam,
    • Alexander E. Urban,
    • Jan O. Korbel,
    • Jason Affourtit,
    • Fabian Grubert,
    • Xueying Chen,
    • Sherman Weissman,
    • Michael Snyder,
    • and Mark B. Gerstein
    Genome Res. December 2008 18: 1865-1874; Published in Advance October 8, 2008, doi:10.1101/gr.081422.108
    .... , Vianna-Morgante, A.M. , Rosenberg, C. , Ignatius, J. , Raynaud, M. , Hollanders, K. , et al. ( 2008 ) Nonrecurrent MECP2 duplications mediated by genomic architecture-driven DNA breaks and break-induced replication repair . Genome Res. 18 : 847 – 858 . ↵ Cheng, Z. , Ventura, M. , She, X. , Khaitovich, P...
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  2. Research: Genome-wide mapping and assembly of structural variant breakpoints in the mouse genome
    • Aaron R. Quinlan,
    • Royden A. Clark,
    • Svetlana Sokolova,
    • Mitchell L. Leibowitz,
    • Yujun Zhang,
    • Matthew E. Hurles,
    • Joshua C. Mell,
    • and Ira M. Hall
    Genome Res. May 2010 20: 623-635; Published in Advance March 22, 2010, doi:10.1101/gr.102970.109
    ...of SV, capture an unprecedented number of variants, and reveal novel breakpoint features. Of mechanistic significance, we report an abundance of complex SVs that appear to be derived from template switching during DNA replication or repair, and a propensity for duplicated genomic regions to generate new...
  3. Research: Recurrence, submicroscopic complexity, and potential clinical relevance of copy gains detected by array CGH that are shown to be unbalanced insertions by FISH
    • Nicholas J. Neill,
    • Blake C. Ballif,
    • Allen N. Lamb,
    • Sumit Parikh,
    • J. Britt Ravnan,
    • Roger A. Schultz,
    • Beth S. Torchia,
    • Jill A. Rosenfeld,
    • and Lisa G. Shaffer
    Genome Res. April 2011 21: 535-544; Published in Advance March 7, 2011, doi:10.1101/gr.114579.110
    ...MJ, Boespflug-Tanguy O, Zenker M, ViannaMorgante AM, Rosenberg C, Ignatius J, Raynaud M, Hollanders K, et al. 2008. Nonrecurrent MECP2 duplications mediated by genomic architecture-driven DNA breaks and break-induced replication repair. Genome Res 18: 847–858. Benito-Sanz S, Thomas NS, Huber C...
  4. Research: RAF gene fusion breakpoints in pediatric brain tumors are characterized by significant enrichment of sequence microhomology
    • Andrew R.J. Lawson,
    • Guy F.L. Hindley,
    • Tim Forshew,
    • Ruth G. Tatevossian,
    • Gabriel A. Jamie,
    • Gavin P. Kelly,
    • Geoffrey A. Neale,
    • Jing Ma,
    • Tania A. Jones,
    • David W. Ellison,
    • and Denise Sheer
    Genome Res. April 2011 21: 505-514; Published in Advance March 10, 2011, doi:10.1101/gr.115782.110
    ...MECP2 duplications mediated by genomic architecture-driven DNA breaks and break-induced replication repair. Genome Res 18: 847–858. Bignell GR, Santarius T, Pole JC, Butler AP, Perry J, Pleasance E, Greenman C, Menzies A, Taylor S, Edkins S, et al. 2007. Architectures of somatic genomic rearrangement...
  5. Resource: Analysis of copy number variations among diverse cattle breeds
    • George E. Liu,
    • Yali Hou,
    • Bin Zhu,
    • Maria Francesca Cardone,
    • Lu Jiang,
    • Angelo Cellamare,
    • Apratim Mitra,
    • Leeson J. Alexander,
    • Luiz L. Coutinho,
    • Maria Elena Dell'Aquila,
    • Lou C. Gasbarre,
    • Gianni Lacalandra,
    • Robert W. Li,
    • Lakshmi K. Matukumalli,
    • Dan Nonneman,
    • Luciana C. de A. Regitano,
    • Tim P.L. Smith,
    • Jiuzhou Song,
    • Tad S. Sonstegard,
    • Curt P. Van Tassell,
    • Mario Ventura,
    • Evan E. Eichler,
    • Tara G. McDaneld,
    • and John W. Keele
    Genome Res. May 2010 20: 693-703; Published in Advance March 8, 2010, doi:10.1101/gr.105403.110
    ...CNV regions identified in normal individuals. These data sets alone correspond to over 910Mb of structurally variant DNA. More than 9000 genes have beenmapped within or near regions of human structural variation. While SNPs aremore frequent,CNVs involvemore genomic sequences andhave potentially more...
  6. Research: Nonallelic homologous recombination between retrotransposable elements is a driver of de novo unbalanced translocations
    • Caroline Robberecht,
    • Thierry Voet,
    • Masoud Zamani Esteki,
    • Beata A. Nowakowska,
    • and Joris R. Vermeesch
    Genome Res. March 2013 23: 411-418; Published in Advance December 3, 2012, doi:10.1101/gr.145631.112
    ...of enhanced subtelomeric coverage in array CGH. Am J Med Genet A 143A: 1850–1857. Bauters M, Van Esch H, Friez MJ, Boespflug-Tanguy O, Zenker M, ViannaMorgante AM, Rosenberg C, Ignatius J, Raynaud M, Hollanders K, et al. 2008. Nonrecurrent MECP2 duplications mediated by genomic architecture-driven DNA breaks...
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