Carvalho, C.M. et al. Complex rearrangements in patients with duplications of MECP2 can occur by fork stalling and template switching. Hum. Mol. Genet. 18, 2188–2203 (2009).
Morrow, D.M., Connelly, C. & Hieter, P. “Break copy” duplication: a model for chromosome fragment formation in Saccharomyces cerevisiae. Genetics 147, 371–382 (1997).
Smith, C.E., Llorente, B. & Symington, L.S. Template switching during break-induced replication. Nature 447, 102–105 (2007).
McEachern, M.J. & Haber, J.E. Break-induced replication and recombinational telomere elongation in yeast. Annu. Rev. Biochem. 75, 111–135 (2006).
Hastings, P.J., Ira, G. & Lupski, J.R. A microhomology-mediated break-induced replication model for the origin of human copy number variation. PLoS Genet. 5, e1000327 (2009).
Hastings, P.J., Lupski, J.R., Rosenberg, S.M. & Ira, G. Mechanisms of change in gene copy number. Nat. Rev. Genet. 10, 551–564 (2009).
Lee, J.A., Carvalho, C.M. & Lupski, J.R. A DNA replication mechanism for generating nonrecurrent rearrangements associated with genomic disorders. Cell 131, 1235–1247 (2007).
Slack, A., Thornton, P.C., Magner, D.B., Rosenberg, S.M. & Hastings, P.J. On the mechanism of gene amplification induced under stress in Escherichia coli. PLoS Genet. 2, e48 (2006).
del Gaudio, D. et al. Increased MECP2 gene copy number as the result of genomic duplication in neurodevelopmentally delayed males. Genet. Med. 8, 784–792 (2006).
Small, K., Iber, J. & Warren, S.T. Emerin deletion reveals a common X-chromosome inversion mediated by inverted repeats. Nat. Genet. 16, 96–99 (1997).
Deem, A. et al. Break-induced replication is highly inaccurate. PLoS Biol. 9, e1000594 (2011).
Lee, J.A. et al. Spastic paraplegia type 2 associated with axonal neuropathy and apparent PLP1 position effect. Ann. Neurol. 59, 398–403 (2006).
Ramocki, M.B., Tavyev, Y.J. & Peters, S.U. The MECP2 duplication syndrome. Am. J. Med. Genet. A. 152A, 1079–1088 (2010).
Bailey, J.A. et al. Recent segmental duplications in the human genome. Science 297, 1003–1007 (2002).
Hu, X.Y., Ray, P.N., Murphy, E.G., Thompson, M.W. & Worton, R.G. Duplicational mutation at the Duchenne muscular dystrophy locus: its frequency, distribution, origin, and phenotype-genotype correlation. Am. J. Hum. Genet. 46, 682–695 (1990).
Mimault, C. et al. Proteolipoprotein gene analysis in 82 patients with sporadic Pelizaeus-Merzbacher disease: duplications, the major cause of the disease, originate more frequently in male germ cells, but point mutations do not. The Clinical European Network on Brain Dysmyelinating Disease. Am. J. Hum. Genet. 65, 360–369 (1999).
Whibley, A.C. et al. Fine-scale survey of X chromosome copy number variants and indels underlying intellectual disability. Am. J. Hum. Genet. 87, 173–188 (2010).
Bartsch, O. et al. Four unrelated patients with Lubs X-linked mental retardation syndrome and different Xq28 duplications. Am. J. Med. Genet. A. 152A, 305–312 (2010).
Lieber, M.R. The mechanism of human nonhomologous DNA end joining. J. Biol. Chem. 283, 1–5 (2008).
Sheen, C.R. et al. Double complex mutations involving F8 and FUNDC2 caused by distinct break-induced replication. Hum. Mutat. 28, 1198–1206 (2007).
Zhang, F., Carvalho, C.M. & Lupski, J.R. Complex human chromosomal and genomic rearrangements. Trends Genet. 25, 298–307 (2009).
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).
Yatsenko, S.A. et al. Molecular mechanisms for subtelomeric rearrangements associated with the 9q34.3 microdeletion syndrome. Hum. Mol. Genet. 18, 1924–1936 (2009).
Vialard, F. et al. Mechanism of intrachromosomal triplications 15q11-q13: a new clinical report. Am. J. Med. Genet. A. 118A, 229–234 (2003).
Wang, J. et al. Intrachromosomal triplication of 2q11.2-q21 in a severely malformed infant: case report and review of triplications and their possible mechanism. Am. J. Med. Genet. 82, 312–317 (1999).
Reddy, K.S. & Logan, J.J. Intrachromosomal triplications: molecular cytogenetic and clinical studies. Clin. Genet. 58, 134–141 (2000).
Lebofsky, R. & Bensimon, A. DNA replication origin plasticity and perturbed fork progression in human inverted repeats. Mol. Cell Biol. 25, 6789–6797 (2005).
Voineagu, I., Narayanan, V., Lobachev, K.S. & Mirkin, S.M. Replication stalling at unstable inverted repeats: interplay between DNA hairpins and fork stabilizing proteins. Proc. Natl. Acad. Sci. USA 105, 9936–9941 (2008).
Paek, A.L. et al. Fusion of nearby inverted repeats by a replication-based mechanism leads to formation of dicentric and acentric chromosomes that cause genome instability in budding yeast. Genes Dev. 23, 2861–2875 (2009).
Mizuno, K., Lambert, S., Baldacci, G., Murray, J.M. & Carr, A.M. Nearby inverted repeats fuse to generate acentric and dicentric palindromic chromosomes by a replication template exchange mechanism. Genes Dev. 23, 2876–2886 (2009).
Kitamura, E., Blow, J.J. & Tanaka, T.U. Live-cell imaging reveals replication of individual replicons in eukaryotic replication factories. Cell 125, 1297–1308 (2006).
Mirkin, E.V. & Mirkin, S.M. Mechanisms of transcription-replication collisions in bacteria. Mol. Cell Biol. 25, 888–895 (2005).
Merrikh, H., Machon, C., Grainger, W.H., Grossman, A.D. & Soultanas, P. Co-directional replication-transcription conflicts lead to replication restart. Nature 470, 554–557 (2011).
Cáceres, M., Sullivan, R.T. & Thomas, J.W. A recurrent inversion on the eutherian X chromosome. Proc. Natl. Acad. Sci. USA 104, 18571–18576 (2007).
Lee, J.A., Cheung, S.W., Ward, P.A., Inoue, K. & Lupski, J.R. Prenatal diagnosis of PLP1 copy number by array comparative genomic hybridization. Prenat. Diagn. 25, 1188–1191 (2005).
Singleton, A.B. et al. α-Synuclein locus triplication causes Parkinson's disease. Science 302, 841 (2003).
Beunders, G. et al. A triplication of the Williams-Beuren syndrome region in a patient with mental retardation, a severe expressive language delay, behavioral problems and dysmorphisms. J. Med. Genet. 47, 271–275 (2010).
Lee, J.A. et al. Role of genomic architecture in PLP1 duplication causing Pelizaeus-Merzbacher disease. Hum. Mol. Genet. 15, 2250–2265 (2006).
Allen, R.C., Zoghbi, H.Y., Moseley, A.B., Rosenblatt, H.M. & Belmont, J.W. Methylation of HpaII and HhaI sites near the polymorphic CAG repeat in the human androgen-receptor gene correlates with X chromosome inactivation. Am. J. Hum. Genet. 51, 1229–1239 (1992).
Ramocki, M.B. et al. Autism and other neuropsychiatric symptoms are prevalent in individuals with MECP2 duplication syndrome. Ann. Neurol. 66, 771–782 (2009).
Barrett, J.C., Fry, B., Maller, J. & Daly, M.J. Haploview: analysis and visualization of LD and haplotype maps. Bioinformatics 21, 263–265 (2005).