[1] | Iafrate AJ, Feuk L, Rivera MN, Listewnik ML, Donahoe PK, et al. (2004) Detection of large-scale variation in the human genome. Nat Genet 36: 949–951.
|
[2] | Korbel JO, Urban AE, Affourtit JP, Godwin B, Grubert F, et al. (2007) Paired-end mapping reveals extensive structural variation in the human genome. Science 318: 420–426.
|
[3] | Sebat J, Lakshmi B, Troge J, Alexander J, Young J, et al. (2004) Large-scale copy number polymorphism in the human genome. Science 305: 525–528.
|
[4] | Redon R, Ishikawa S, Fitch KR, Feuk L, Perry GH, et al. (2006) Global variation in copy number in the human genome. Nature 444: 444–454.
|
[5] | Wong KK, deLeeuw RJ, Dosanjh NS, Kimm LR, Cheng Z, et al. (2007) A comprehensive analysis of common copy-number variations in the human genome. Am J Hum Genet 80: 91–104.
|
[6] | Khaja R, Zhang J, MacDonald JR, He Y, Joseph-George AM, et al. (2006) Genome assembly comparison identifies structural variants in the human genome. Nat Genet 38: 1413–1418.
|
[7] | Newman TL, Tuzun E, Morrison VA, Hayden KE, Ventura M, et al. (2005) A genome-wide survey of structural variation between human and chimpanzee. Genome Res 15: 1344–1356.
|
[8] | Fiegler H, Redon R, Andrews D, Scott C, Andrews R, et al. (2006) Accurate and reliable high-throughput detection of copy number variation in the human genome. Genome Res 16: 1566–1574.
|
[9] | Komura D, Shen F, Ishikawa S, Fitch KR, Chen W, et al. (2006) Genome-wide detection of human copy number variations using high-density DNA oligonucleotide arrays. Genome Res 16: 1575–1584.
|
[10] | Lupski JR (2007) Structural variation in the human genome. N Engl J Med 356: 1169–1171.
|
[11] | Tuzun E, Sharp AJ, Bailey JA, Kaul R, Morrison VA, et al. (2005) Fine-scale structural variation of the human genome. Nat Genet 37: 727–732.
|
[12] | Bruder CEG, Poitrowski A, Gijsbers AACJ, Andersson R, Erickson S, et al. (2008) Phenotypically concordant and discordant monozygotic twins display different DNA copy-number-variation profiles. Am J Hum Genet 82: 1–9.
|
[13] | Dumas L, Kim YH, Karimpour-Fard A, Cox M, Hopkins J, et al. (2007) Gene copy number variation spanning 60 million years of human and primate evolution. Genome Res 17: 1266–1277.
|
[14] | Nahon JL (2003) Birth of ‘human-specific’ genes during primate evolution. Genetica 118: 193–208.
|
[15] | Bailey JA, Eichler EE (2006) Primate segmental duplications: crucibles of evolution, diversity and disease. Nat Rev Genet 7: 552–564.
|
[16] | Stankiewicz P, Shaw CJ, Withers M, Inoue K, Lupski JR (2004) Serial segmental duplications during primate evolution result in complex human genome architecture. Genome Res 14: 2209–2220.
|
[17] | Lupski JR (1998) Genomic disorders: structural features of the genome can lead to DNA rearrangement and human disease traits. Trends Genet 14: 417–422.
|
[18] | Stankiewicz P, Lupski JR (2002) Genome architecture, rearrangements and genomic disorders. Trends Genet 18: 74–82.
|
[19] | Shaw CJ, Lupski JR (2005) Non-recurrent 17p11.2 deletions are generated by homologous and non-homologous mechanisms. Hum Genet 116: 1–7.
|
[20] | Lupski JR, Stankiewicz P (2005) Genomic disorders: molecular mechanisms for rearrangements and conveyed phenotypes. PLoS Genet 1: e49. doi:10.1371/journal.pgen.0010049.
|
[21] | Lupski JR (2006) Genome structural variation and sporadic disease traits. Nat Genet 38: 974–976.
|
[22] | Lee JA, Carvalho CM, Lupski JR (2007) A DNA replication mechanism for generating nonrecurrent rearrangements associated with genomic disorders. Cell 131: 1235–1247.
|
[23] | Nobile CT, Rizzi L, Simionati F, Nigro B, Cardazzo V, Patarnello B, Valle T, Danieli G, GA (2002) Analysis of 22 deletion breakpoints in dystrophin intron 49. Hum Genet 110: 418–421.
|
[24] | Inoue K, Osaka H, Thurston VC, Clarke JT, Yoneyama A, et al. (2002) Genomic rearrangements resulting in PLP1 deletion occur by nonhomologous end joining and cause different dysmyelinating phenotypes in males and females. Am J Hum Genet 71: 838–853.
|
[25] | Lee JA (2006) Molecular analysis of the non-recurrent genomic duplications causing Pelizaeus-Merzbacher disease and its allelic disorder paraplegia type 2. [PhD thesis] Houston (Texas): Department of Molecular and Human Genetics, Baylor College of Medicine.
|
[26] | Potocki LB, W, Treadwell-Deering D, Carvalho CM, Eifert A, Friedman EM, et al. (2007) Characterization of Potocki-Lupski syndrome (dup(17)(p11.2p11.2)) and delineation of a dosage-sensitive critical interval that can convey an autism phenotype. Am J Hum Genet 80: 633–649.
|
[27] | Vissers LE, Stankiewicz P, Yatsenko SA, Crawford E, Creswick H, et al. (2007) Complex chromosome 17p rearrangements associated with low-copy repeats in two patients with congenital anomalies. Hum Genet 121: 697–709.
|
[28] | Chen JM, Chuzhanova N, Stenson PD, Férec C, Cooper DN (2005) Intrachromosomal serial replication slippage in trans gives rise to diverse genomic rearrangements involving inversions. Hum Mutat 26: 362–373.
|
[29] | Férec C, Casals T, Chuzhanova N, Macek MJ, Bienvenu T, et al. (2006) Gross genomic rearrangements involving deletions in the CFTR gene: characterization of six new events from a large cohort of hitherto unidentified cystic fibrosis chromosomes and meta-analysis of the underlying mechanisms. Eur J Hum Genet 14: 562–567.
|
[30] | del Gaudio D, Fang P, Scaglia F, Ward PA, Craigen WJ, et al. (2006) Increased MECP2 gene copy number as the result of genomic duplication in neurodevelopmentally delayed males. Genet Med 8: 784–792.
|
[31] | Sheen CR, Jewell UR, Morris CM, Brennan SO, Férec C, et al. (2007) Double complex mutations involving F8 and FUNDC2 caused by distinct break-induced replication. Hum Mutat 28: 1198–2006.
|
[32] | Stankiewicz P, Shaw CJ, Dapper JD, Wakui K, Shaffer LG, et al. (2003) Genome architecture catalyzes nonrecurrent chromosomal rearrangements. Am J Hum Genet 72: 1101–1116.
|
[33] | Lee JA, Inoue K, Cheung SW, Shaw CA, Stankiewicz P, et al. (2006) Role of genomic architecture in PLP1 duplication causing Pelizaeus-Merzbacher disease. Hum Mol Genet 15: 2250–2265.
|
[34] | Lee JA, Madrid RE, Sperle K, Ritterson CM, Hobson GM, et al. (2006) Spastic paraplegia type 2 associated with axonal neuropathy and apparent PLP1 position effect. Ann Neurol 59: 398–403.
|
[35] | Slack A, Thornton PC, Magner DB, Rosenberg SM, Hastings PJ (2006) On the mechanism of gene amplification induced under stress in Escherichia coli. PLoS Genet 2: e48. doi:10.1371/journal.pgen.0020048.
|
[36] | Volik S, Raphael BJ, Huang G, Stratton MR, Bignel G, et al. (2006) Decoding the fine-scale structure of a breast cancer genome and transcriptome. Genome Res 16: 394–404.
|
[37] | Bignell GR, Santarius T, Pole JC, Butler AP, Perry J, et al. (2007) Architectures of somatic genomic rearrangement in human cancer amplicons at sequence-level resolution. Genome Res 17: 1296–1303.
|
[38] | Canning S, Dryja TP (1989) Short, direct repeats at the breakpoints of deletions of the retinoblastoma gene. Proc Natl Acad Sci U S A 86: 5044–5048.
|
[39] | Kohno T, Yokata J (2006) Molecular processes of chromosome 9p21 deletions causing inactivation of the p16 tumor suppressor gene in human cancer: deduction from structural analysis of breakpoints for deletions. DNA Repair (Amst) 5: 1273–1281.
|
[40] | Zhang Y, Zeleznik-Le N, Emmanuel N, Jayathilaka N, Chen J, et al. (2004) Characterization of genomic breakpoints in MLL and CBP in leukemia patients with t(11;16). Genes Chromosomes Cancer 41: 257–265.
|
[41] | Zhang Y, Strissel P, Strick R, Chen J, Nucifora G, et al. (2004) Genomic DNA breakpoints in AML1/RUNX1 and ETO cluster with topoisomerase II DNA cleavage and DNase I hypersensitive sites in t(8;21) leukemia. Proc Natl Acad Sci U S A 99: 3070–3075.
|
[42] | Chen C, Umezu K, Kolodner RD (1998) Chromosomal rearrangements occur in S. cerevisiae rfa1 mutator mutants due to mutagenic lesions processed by double-strand-break repair. Mol Cell 2: 9–22.
|
[43] | Cairns J, Foster PL (1991) Adaptive reversion of a frameshift mutation in Escherichia coli. Genetics 128: 695–701.
|
[44] | Hastings PJ, Bull HJ, Klump JR, Rosenberg SM (2000) Adaptive amplification: an inducible chromosomal instability mechanism. Cell 103: 723–731.
|
[45] | Hastings PJ, Slack A, Petrosino JF, Rosenberg SM (2004) Adaptive amplification and point mutation are independent mechanisms: Evidence for various stress-inducible mutation mechanisms. PLoS Biol 2: e399. doi:10.1371/journal.pbio.0020399.
|
[46] | Kugelberg E, Kofoid E, Reams AB, Andersson DI, Roth JR (2006) Multiple pathways of selected gene amplification during adaptive mutation. Proc Natl Acad Sci U S A 103: 17319–17324.
|
[47] | Hastings PJ (2007) Adaptive amplification. Critical Rev Biochem Mol Biol 42: 1–13.
|
[48] | Friedberg EC, Walker GC, Siede W, Wood RD, Schultz RA, et al. (2005) DNA Repair and Mutagenesis. Washington (DC): ASM Press.
|
[49] | Ikeda H, Shimizu H, Ukita T, Kumagai M (1995) A novel assay for illegitimate recombination in Escherichia coli: stimulation of lambda bio transducing phage formation by ultra-violet light and its independence from RecA function. Adv Biophys 31: 197–208.
|
[50] | Albertini AM, Hofer M, Calos MP, Miller JH (1982) On the formation of spontaneous deletions: the importance of short sequence homologies in the generation of large deletions. Cell 29: 319–328.
|
[51] | Farabaugh PJ, Schmeissner U, Hofer M, Miller JH (1978) Genetic studies of the lac repressor. VII. On the molecular nature of spontaneous hotspots in the lacI gene of Escherichia coli. J Mol Biol 126: 847–857.
|
[52] | Shimizu H, Yamaguchi H, Ashizawa Y, Kohno Y, Asami M, et al. (1997) Short-homology-independent illegitimate recombination in Escherichia coli: distinct mechanism from short-homology-dependent illegitimate recombination. J Mol Biol 266: 297–305.
|
[53] | Bzymek M, Lovett ST (2001) Instability of repetitive DNA sequences: the role of replication in multiple mechanisms. Proc Natl Acad Sci U S A 98: 8319–8325.
|
[54] | Ponder RG, Fonville NC, Rosenberg SM (2005) A switch from high-fidelity to error-prone DNA double-strand break repair underlies stress-induced mutation. Mol Cell 19: 791–804.
|
[55] | Payen C, Koszul R, Dujon B, Fischer G (2008) Segmental duplications arise from Pol32-dependent repair of broken forks through two alternative replication-based mechanisms. PLoS Genet 4: e1000175. doi:10.1371/journal.pgen.1000175.
|
[56] | Branzei D, Foiani M (2007) Template Switching: From Replication Fork Repair to Genome Rearrangements. Cell 131: 1228–1230.
|
[57] | Merrihew RV, Marburger K, Pennington SL, Roth DB, Wilson JH (1996) High-frequency illegitimate integration of transfected DNA at preintegrated target sites in a mammalian genome. Mol Cell Biol 16: 10–18.
|
[58] | Morrow DM, Connelly C, Hieter P (1997) “Break-copy” duplication: a model for chromosome fragment formation in Saccharomyces cerevisiae. Genetics 147: 371–382.
|
[59] | McEachern MJ, Haber JE (2006) Break-Induced Replication and Recombinational Telomere Elongation in Yeast. Annu Rev Biochem 75: 111–135.
|
[60] | Smith CE, Llorente B, Symington LS (2007) Template switching during break-induced replication. Nature 447: 102–105.
|
[61] | Lydeard JR, Jain S, Yamaguchi M, Haber JE (2007) Break-induced replication and telomerase-independent telomere maintenance require Pol32. Nature 448: 820–823.
|
[62] | Motamedi M, Szigety SK, Rosenberg SM (1999) Double-strand-break repair in Escherichia coli: physical evidence for a DNA replication mechanism in vivo. Genes Dev 13: 2889–2903.
|
[63] | Llorente B, Smith CE, Symington LS (2008) Break-induced replication: what is it and what is it for? Cell Cycle 7: 859–864.
|
[64] | Heiter P, Mann C, Snyder M, Davis RW (1985) Mitotic stability of yeast chromosomes: A colony color assay that measures nondisjunction and chromosome loss. Cell 40: 381–392.
|
[65] | Deem A, Barker K, Vanhulle K, Downing B, Vayl A, et al. (2008) Defective break-induced replication leads to half-crossovers in Saccharomyces cerevisiae. Genetics 179: 1845–1860.
|
[66] | Schmidt KH, Wu J, Kolodner RD (2006) Control of translocations between highly diverged genes by Sgs1, the Saccharomyces cerevisiae homolog of the Bloom's syndrome protein. Mol Cell Biol 26: 5406–5420.
|
[67] | Bauters M, Van Esch H, Friez MJ, Boespflug-Tanguy O, Zenker M, et al. (2008) Nonrecurrent MECP2 duplications mediated by genomic architecture-driven DNA breaks and break-induced replication repair. Genome Res 18: 847–858.
|
[68] | Lovett ST, Hurley RL, Sutera VA Jr, Aubuchon RH, Lebedeva MA (2002) Crossing over between regions of limited homology in Escherichia coli. RecA-dependent and RecA-independent pathways. Genetics 160: 851–859.
|
[69] | Liskay RM, Letsou A, Stachelek JL (1987) Homology requirement for efficient gene conversion between duplicated chromosomal sequences in mammalian cells. Genetics 115: 161–167.
|
[70] | Reiter LT, Hastings PJ, Nelis E, De Jonghe P, Van Broeckhoven C, et al. (1998) Human meiotic recombination products revealed by sequencing a hotspot for homologous strand exchange in multiple HNPP deletion patients. Am J Hum Genet 62: 1023–1033.
|
[71] | VanHulle K, Lemoine FJ, Narayanan V, Downing B, Hull K, et al. (2007) Inverted DNA repeats channel repair of distant double-strand breaks into chromatid fusions and chromosomal rearrangements. Mol Cell Biol 27: 2601–2614.
|
[72] | Davis AP, Symington LS (2004) RAD51-dependent break-induced replication in yeast. Mol Cell Biol 24: 2344–2351.
|
[73] | Le S, Moore JK, Haber JE, Greider CW (1999) RAD50 and RAD51 define two pathways that collaborate to maintain telomeres in the absence of telomerase. Genetics 152: 143–152.
|
[74] | Teng SC, Zakian VA (1999) Telomere-telomere recombination is an efficient bypass pathway for telomere maintenance in Saccharomyces cerevisiae. Mol Cell Biol 19: 8083–8093.
|
[75] | Bentley J, Diggle CP, Harnden P, Knowles MA, Kiltie AE (2004) DNA double strand break repair in human bladder cancer is error prone and involves microhomology-associated end-joining. Nucleic Acids Res 32: 5249–5259.
|
[76] | Corneo B, Wendland RL, Deriano L, Cui X, Klein IA, et al. (2007) Rag mutations reveal robust alternative end joining. Nature 449: 483–486.
|
[77] | Lisby M, Barlow JH, Burgess RC, Rothstein R (2004) Choreography of the DNA damage response: spatiotemporal relationships among checkpoint and repair proteins. Cell 118: 699–713.
|
[78] | Pennington JM, Rosenberg SM (2007) Spontaneous DNA breakage in single living cells of Escherichia coli. Nat Gen 39: 797–802.
|
[79] | Saleh-Gohari N, Bryant HE, Schultz N, Parker KM, Cassel TN, et al. (2005) Spontaneous homologous recombination is induced by collapsed replication forks that are caused by endogenous DNA single-strand breaks. Mol Cell Biol 25: 7158–7169.
|
[80] | McIlwraith MJ, Vaisman A, Liu Y, Fanning E, Woodgate R, et al. (2005) Human DNA polymerase eta promotes DNA synthesis from strand invasion intermediates of homologous recombination. Mol Cell 20: 783–792.
|
[81] | Kawamoto T, Araki K, Sonoda E, Yamashita YM, Harada K, et al. (2005) Dual roles for DNA polymerase eta in homologous DNA recombination and translesion DNA synthesis. Mol Cell 20: 793–799.
|
[82] | Cannistraro VJ, Taylor JS (2007) Ability of polymerase eta and T7 DNA polymerase to bypass bulge structures. J Biol Chem 282: 11188–11196.
|
[83] | Roth DB, Chang XB, Wilson JH (1989) Comparison of filler DNA at immune, nonimmune, and oncogenic rearrangements suggests multiple mechanisms of formation. Mol Cell Biol 9: 3049–3057.
|
[84] | Young SD, Marshall RS, Hill RP (1988) Hypoxia induces DNA overreplication and enhances metastatic potential of murine tumor cells. Proc Natl Acad Sci U S A 85: 9533–9537.
|
[85] | Coquelle A, Toledo F, Stern S, Bieth A, Debatisse M (1998) A new role for hypoxia in tumor progression: induction of fragile site triggering genomic rearrangements and formation of complex DMs and HSRs. Mol Cell 2: 259–265.
|
[86] | Subarsky P, Hill RP (2003) The hypoxic tumour microenvironment and metastatic progression. Clin Exp Metastasis 20: 237–250.
|
[87] | Bindra RSS, Chaffer PJ, Meng A, Woo J, M?seide K, et al. (2004) Down-regulation of Rad51 and decreased homologous recombination in hypoxic cancer cells. Mol Cell Biol 24: 8504–8518.
|
[88] | Bindra RS, Glazer PM (2007) Repression of RAD51 gene expression by E2F4/p130 complexes in hypoxia. Oncogene 26: 2048–2057.
|
[89] | Huang LE, Bindra RS, Glazer PM, Harris AL (2007) Hypoxia-induced genetic instability–a calculated mechanism underlying tumor progression. J Mol Med 85: 139–148.
|
[90] | Bindra RS, Crosby ME, Glazer PM (2007) Regulation of DNA repair in hypoxic cancer cells. Cancer Metastasis Rev 26: 249–260.
|
[91] | McVey M, Adams M, Staeva-Vieira E, Sekelsky JJ (2004) Evidence for multiple cycles of strand invasion during repair of double-strand gaps in Drosophila. Genetics 167: 699–705.
|
[92] | Bindra RS, Glazer PM (2007) Co-repression of mismatch repair gene expression by hypoxia in cancer cells: role of the Myc/Max network. Cancer Lett 252: 93–103.
|
[93] | Mihaylova VT, Bindra RS, Yuan J, Campisi D, Narayanan L, et al. (2003) Decreased expression of the DNA mismatch repair gene Mlh1 under hypoxic stress in mammalian cells. Mol Cell Biol 23: 3265–3273.
|
[94] | Myung K, Chen C, Kolodner RD (2001) Multiple pathways cooperate in the suppression of genome instability in Saccharomyces cerevisiae. Nature 411: 1073–1076.
|
[95] | Lombardo M-J, Aponyi I, Rosenberg SM (2004) General stress response regulator RpoS in adaptive mutation and amplification in Escherichia coli. Genetics 166: 669–680.
|
[96] | Fishman-Lobell J, Haber JE (1992) Removal of nonhomologous DNA ends in double-strand break recombination: the role of the yeast ultraviolet repair gene RAD1. Science 258: 480–484.
|
[97] | Mortensen UH, Bendixen HC, Sunjevaric I, Rothstein R (1996) DNA strand annealing is promoted by yeast Rad52 protein. Proc Natl Acad Sci U S A 93: 10729–10734.
|
[98] | Tsukamoto Y, Kato J, Ikeda H (1996) Effects of mutations of RAD50, RAD51, RAD52, and related genes on illegitimate recombination in Saccharomyces cerevisiae. Genetics 142: 383–391.
|
[99] | Wu Y, Kantake N, Sugiyama T, Kowalczykowski SC (2008) Rad51 protein controls Rad52-mediated DNA annealing. J Biol Chem 283: 14883–14892.
|
[100] | Lee K, Lee SE (2007) Saccharomyces cerevisiae Sae2- and Tel1-dependent single-strand DNA formation at DNA break promotes microhomology-mediated end joining. Genetics 176: 2003–2014.
|
[101] | Lupski JR (2007) An evolution revolution provides further revelation. Bioessays 29: 1182–1184.
|
[102] | Ohno S (1970) Evolution by gene duplication. Berlin, New York: Springer-Verlag.
|
[103] | Hurles M (2004) Gene duplication: the genomic trade in spare parts. PLoS Biol 2: e206. doi:10.1371/journal.pbio.0020206.
|
[104] | Hittinger CT, Carroll SB (2007) Gene duplication and the adaptive evolution of a classic genetic switch. Nature 449: 677–681.
|
[105] | Spence JE, Perciaccante RG, Greig GM, Willard HF, Ledbetter DH, et al. (1988) Uniparental disomy as a mechanism for human genetic disease. Am J Hum Genet 42: 217–226.
|
[106] | Lee JA, Lupski JR (2006) Genomic rearrangements and gene copy-number alterations as a cause of nervous system disorders. Neuron 52: 103–121.
|