{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,19]],"date-time":"2026-10-19T13:24:06Z","timestamp":1792416246519,"version":"4.4.0"},"reference-count":106,"publisher":"Public Library of Science (PLoS)","issue":"1","license":[{"start":{"date-parts":[[2009,1,30]],"date-time":"2009-01-30T00:00:00Z","timestamp":1233273600000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["www.plosgenetics.org"],"crossmark-restriction":false},"short-container-title":["PLoS Genet"],"DOI":"10.1371\/journal.pgen.1000327","type":"journal-article","created":{"date-parts":[[2009,1,29]],"date-time":"2009-01-29T17:52:50Z","timestamp":1233251570000},"page":"e1000327","update-policy":"https:\/\/doi.org\/10.1371\/journal.pgen.corrections_policy","source":"Crossref","is-referenced-by-count":770,"title":["A Microhomology-Mediated Break-Induced Replication Model for the Origin of Human Copy Number Variation"],"prefix":"10.1371","volume":"5","author":[{"given":"P. J.","family":"Hastings","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Grzegorz","family":"Ira","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"James R.","family":"Lupski","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2009,1,30]]},"reference":[{"key":"ref1","doi-asserted-by":"crossref","first-page":"949","DOI":"10.1038\/ng1416","article-title":"Detection of large-scale variation in the human genome.","volume":"36","author":"AJ Iafrate","year":"2004","journal-title":"Nat Genet"},{"key":"ref2","doi-asserted-by":"crossref","first-page":"420","DOI":"10.1126\/science.1149504","article-title":"Paired-end mapping reveals extensive structural variation in the human genome.","volume":"318","author":"JO Korbel","year":"2007","journal-title":"Science"},{"key":"ref3","doi-asserted-by":"crossref","first-page":"525","DOI":"10.1126\/science.1098918","article-title":"Large-scale copy number polymorphism in the human genome.","volume":"305","author":"J Sebat","year":"2004","journal-title":"Science"},{"key":"ref4","doi-asserted-by":"crossref","first-page":"444","DOI":"10.1038\/nature05329","article-title":"Global variation in copy number in the human genome.","volume":"444","author":"R Redon","year":"2006","journal-title":"Nature"},{"key":"ref5","doi-asserted-by":"crossref","first-page":"91","DOI":"10.1086\/510560","article-title":"A comprehensive analysis of common copy-number variations in the human genome.","volume":"80","author":"KK Wong","year":"2007","journal-title":"Am J Hum Genet"},{"key":"ref6","doi-asserted-by":"crossref","first-page":"1413","DOI":"10.1038\/ng1921","article-title":"Genome assembly comparison identifies structural variants in the human genome.","volume":"38","author":"R Khaja","year":"2006","journal-title":"Nat Genet"},{"key":"ref7","doi-asserted-by":"crossref","first-page":"1344","DOI":"10.1101\/gr.4338005","article-title":"A genome-wide survey of structural variation between human and chimpanzee.","volume":"15","author":"TL Newman","year":"2005","journal-title":"Genome Res"},{"key":"ref8","doi-asserted-by":"crossref","first-page":"1566","DOI":"10.1101\/gr.5630906","article-title":"Accurate and reliable high-throughput detection of copy number variation in the human genome.","volume":"16","author":"H Fiegler","year":"2006","journal-title":"Genome Res"},{"key":"ref9","doi-asserted-by":"crossref","first-page":"1575","DOI":"10.1101\/gr.5629106","article-title":"Genome-wide detection of human copy number variations using high-density DNA oligonucleotide arrays.","volume":"16","author":"D Komura","year":"2006","journal-title":"Genome Res"},{"key":"ref10","doi-asserted-by":"crossref","first-page":"1169","DOI":"10.1056\/NEJMcibr067658","article-title":"Structural variation in the human genome.","volume":"356","author":"JR Lupski","year":"2007","journal-title":"N Engl J Med"},{"key":"ref11","doi-asserted-by":"crossref","first-page":"727","DOI":"10.1038\/ng1562","article-title":"Fine-scale structural variation of the human genome.","volume":"37","author":"E Tuzun","year":"2005","journal-title":"Nat Genet"},{"key":"ref12","first-page":"1","article-title":"Phenotypically concordant and discordant monozygotic twins display different DNA copy-number-variation profiles.","volume":"82","author":"CEG Bruder","year":"2008","journal-title":"Am J Hum Genet"},{"key":"ref13","doi-asserted-by":"crossref","first-page":"1266","DOI":"10.1101\/gr.6557307","article-title":"Gene copy number variation spanning 60 million years of human and primate evolution.","volume":"17","author":"L Dumas","year":"2007","journal-title":"Genome Res"},{"key":"ref14","doi-asserted-by":"crossref","first-page":"193","DOI":"10.1023\/A:1024157714736","article-title":"Birth of \u2018human-specific\u2019 genes during primate evolution.","volume":"118","author":"JL Nahon","year":"2003","journal-title":"Genetica"},{"key":"ref15","doi-asserted-by":"crossref","first-page":"552","DOI":"10.1038\/nrg1895","article-title":"Primate segmental duplications: crucibles of evolution, diversity and disease.","volume":"7","author":"JA Bailey","year":"2006","journal-title":"Nat Rev Genet"},{"key":"ref16","doi-asserted-by":"crossref","first-page":"2209","DOI":"10.1101\/gr.2746604","article-title":"Serial segmental duplications during primate evolution result in complex human genome architecture.","volume":"14","author":"P Stankiewicz","year":"2004","journal-title":"Genome Res"},{"key":"ref17","doi-asserted-by":"crossref","first-page":"417","DOI":"10.1016\/S0168-9525(98)01555-8","article-title":"Genomic disorders: structural features of the genome can lead to DNA rearrangement and human disease traits.","volume":"14","author":"JR Lupski","year":"1998","journal-title":"Trends Genet"},{"key":"ref18","doi-asserted-by":"crossref","first-page":"74","DOI":"10.1016\/S0168-9525(02)02592-1","article-title":"Genome architecture, rearrangements and genomic disorders.","volume":"18","author":"P Stankiewicz","year":"2002","journal-title":"Trends Genet"},{"key":"ref19","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1007\/s00439-004-1204-9","article-title":"Non-recurrent 17p11.2 deletions are generated by homologous and non-homologous mechanisms.","volume":"116","author":"CJ Shaw","year":"2005","journal-title":"Hum Genet"},{"key":"ref20","doi-asserted-by":"crossref","first-page":"e49","DOI":"10.1371\/journal.pgen.0010049","article-title":"Genomic disorders: molecular mechanisms for rearrangements and conveyed phenotypes.","volume":"1","author":"JR Lupski","year":"2005","journal-title":"PLoS Genet"},{"key":"ref21","doi-asserted-by":"crossref","first-page":"974","DOI":"10.1038\/ng0906-974","article-title":"Genome structural variation and sporadic disease traits.","volume":"38","author":"JR Lupski","year":"2006","journal-title":"Nat Genet"},{"key":"ref22","doi-asserted-by":"crossref","first-page":"1235","DOI":"10.1016\/j.cell.2007.11.037","article-title":"A DNA replication mechanism for generating nonrecurrent rearrangements associated with genomic disorders.","volume":"131","author":"JA Lee","year":"2007","journal-title":"Cell"},{"key":"ref23","doi-asserted-by":"crossref","first-page":"418","DOI":"10.1007\/s00439-002-0721-7","article-title":"Analysis of 22 deletion breakpoints in dystrophin intron 49.","volume":"110","author":"CT Nobile","year":"2002","journal-title":"Hum Genet"},{"key":"ref24","doi-asserted-by":"crossref","first-page":"838","DOI":"10.1086\/342728","article-title":"Genomic rearrangements resulting in PLP1 deletion occur by nonhomologous end joining and cause different dysmyelinating phenotypes in males and females.","volume":"71","author":"K Inoue","year":"2002","journal-title":"Am J Hum Genet"},{"key":"ref25","first-page":"371","article-title":"Molecular analysis of the non-recurrent genomic duplications causing Pelizaeus-Merzbacher disease and its allelic disorder paraplegia type 2.","author":"JA Lee","year":"2006"},{"key":"ref26","doi-asserted-by":"crossref","first-page":"633","DOI":"10.1086\/512864","article-title":"Characterization of Potocki-Lupski syndrome (dup(17)(p11.2p11.2)) and delineation of a dosage-sensitive critical interval that can convey an autism phenotype.","volume":"80","author":"LB, W Potocki","year":"2007","journal-title":"Am J Hum Genet"},{"key":"ref27","doi-asserted-by":"crossref","first-page":"697","DOI":"10.1007\/s00439-007-0359-6","article-title":"Complex chromosome 17p rearrangements associated with low-copy repeats in two patients with congenital anomalies.","volume":"121","author":"LE Vissers","year":"2007","journal-title":"Hum Genet"},{"key":"ref28","doi-asserted-by":"crossref","first-page":"362","DOI":"10.1002\/humu.20230","article-title":"Intrachromosomal serial replication slippage in trans gives rise to diverse genomic rearrangements involving inversions.","volume":"26","author":"JM Chen","year":"2005","journal-title":"Hum Mutat"},{"key":"ref29","doi-asserted-by":"crossref","first-page":"562","DOI":"10.1038\/sj.ejhg.5201590","article-title":"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.","volume":"14","author":"C F\u00e9rec","year":"2006","journal-title":"Eur J Hum Genet"},{"key":"ref30","doi-asserted-by":"crossref","first-page":"784","DOI":"10.1097\/01.gim.0000250502.28516.3c","article-title":"Increased MECP2 gene copy number as the result of genomic duplication in neurodevelopmentally delayed males.","volume":"8","author":"D del Gaudio","year":"2006","journal-title":"Genet Med"},{"key":"ref31","doi-asserted-by":"crossref","first-page":"1198","DOI":"10.1002\/humu.20591","article-title":"Double complex mutations involving F8 and FUNDC2 caused by distinct break-induced replication.","volume":"28","author":"CR Sheen","year":"2007","journal-title":"Hum Mutat"},{"key":"ref32","doi-asserted-by":"crossref","first-page":"1101","DOI":"10.1086\/374385","article-title":"Genome architecture catalyzes nonrecurrent chromosomal rearrangements.","volume":"72","author":"P Stankiewicz","year":"2003","journal-title":"Am J Hum Genet"},{"key":"ref33","doi-asserted-by":"crossref","first-page":"2250","DOI":"10.1093\/hmg\/ddl150","article-title":"Role of genomic architecture in PLP1 duplication causing Pelizaeus-Merzbacher disease.","volume":"15","author":"JA Lee","year":"2006","journal-title":"Hum Mol Genet"},{"key":"ref34","doi-asserted-by":"crossref","first-page":"398","DOI":"10.1002\/ana.20732","article-title":"Spastic paraplegia type 2 associated with axonal neuropathy and apparent PLP1 position effect.","volume":"59","author":"JA Lee","year":"2006","journal-title":"Ann Neurol"},{"key":"ref35","doi-asserted-by":"crossref","first-page":"e48","DOI":"10.1371\/journal.pgen.0020048","article-title":"On the mechanism of gene amplification induced under stress in <italic>Escherichia coli<\/italic>.","volume":"2","author":"A Slack","year":"2006","journal-title":"PLoS Genet"},{"key":"ref36","doi-asserted-by":"crossref","first-page":"394","DOI":"10.1101\/gr.4247306","article-title":"Decoding the fine-scale structure of a breast cancer genome and transcriptome.","volume":"16","author":"S Volik","year":"2006","journal-title":"Genome Res"},{"key":"ref37","doi-asserted-by":"crossref","first-page":"1296","DOI":"10.1101\/gr.6522707","article-title":"Architectures of somatic genomic rearrangement in human cancer amplicons at sequence-level resolution.","volume":"17","author":"GR Bignell","year":"2007","journal-title":"Genome Res"},{"key":"ref38","doi-asserted-by":"crossref","first-page":"5044","DOI":"10.1073\/pnas.86.13.5044","article-title":"Short, direct repeats at the breakpoints of deletions of the retinoblastoma gene.","volume":"86","author":"S Canning","year":"1989","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref39","doi-asserted-by":"crossref","first-page":"1273","DOI":"10.1016\/j.dnarep.2006.05.021","article-title":"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.","volume":"5","author":"T Kohno","year":"2006","journal-title":"DNA Repair (Amst)"},{"key":"ref40","doi-asserted-by":"crossref","first-page":"257","DOI":"10.1002\/gcc.20077","article-title":"Characterization of genomic breakpoints in MLL and CBP in leukemia patients with t(11;16).","volume":"41","author":"Y Zhang","year":"2004","journal-title":"Genes Chromosomes Cancer"},{"key":"ref41","doi-asserted-by":"crossref","first-page":"3070","DOI":"10.1073\/pnas.042702899","article-title":"Genomic DNA breakpoints in AML1\/RUNX1 and ETO cluster with topoisomerase II DNA cleavage and DNase I hypersensitive sites in t(8;21) leukemia.","volume":"99","author":"Y Zhang","year":"2004","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref42","doi-asserted-by":"crossref","first-page":"9","DOI":"10.1016\/S1097-2765(00)80109-4","article-title":"Chromosomal rearrangements occur in S. cerevisiae rfa1 mutator mutants due to mutagenic lesions processed by double-strand-break repair.","volume":"2","author":"C Chen","year":"1998","journal-title":"Mol Cell"},{"key":"ref43","doi-asserted-by":"crossref","first-page":"695","DOI":"10.1093\/genetics\/128.4.695","article-title":"Adaptive reversion of a frameshift mutation in <italic>Escherichia coli<\/italic>.","volume":"128","author":"J Cairns","year":"1991","journal-title":"Genetics"},{"key":"ref44","doi-asserted-by":"crossref","first-page":"723","DOI":"10.1016\/S0092-8674(00)00176-8","article-title":"Adaptive amplification: an inducible chromosomal instability mechanism.","volume":"103","author":"PJ Hastings","year":"2000","journal-title":"Cell"},{"key":"ref45","doi-asserted-by":"crossref","first-page":"e399","DOI":"10.1371\/journal.pbio.0020399","article-title":"Adaptive amplification and point mutation are independent mechanisms: Evidence for various stress-inducible mutation mechanisms.","volume":"2","author":"PJ Hastings","year":"2004","journal-title":"PLoS Biol"},{"key":"ref46","doi-asserted-by":"crossref","first-page":"17319","DOI":"10.1073\/pnas.0608309103","article-title":"Multiple pathways of selected gene amplification during adaptive mutation.","volume":"103","author":"E Kugelberg","year":"2006","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref47","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1080\/10409230701507757","article-title":"Adaptive amplification.","volume":"42","author":"PJ Hastings","year":"2007","journal-title":"Critical Rev Biochem Mol Biol"},{"key":"ref48","first-page":"1164","article-title":"DNA Repair and Mutagenesis","author":"EC Friedberg","year":"2005"},{"key":"ref49","doi-asserted-by":"crossref","first-page":"197","DOI":"10.1016\/0065-227X(95)99392-3","article-title":"A novel assay for illegitimate recombination in <italic>Escherichia coli<\/italic>: stimulation of lambda bio transducing phage formation by ultra-violet light and its independence from RecA function.","volume":"31","author":"H Ikeda","year":"1995","journal-title":"Adv Biophys"},{"key":"ref50","doi-asserted-by":"crossref","first-page":"319","DOI":"10.1016\/0092-8674(82)90148-9","article-title":"On the formation of spontaneous deletions: the importance of short sequence homologies in the generation of large deletions.","volume":"29","author":"AM Albertini","year":"1982","journal-title":"Cell"},{"key":"ref51","first-page":"847","article-title":"Genetic studies of the lac repressor. VII. On the molecular nature of spontaneous hotspots in the lacI gene of Escherichia coli.","volume":"126","author":"PJ Farabaugh","year":"1978","journal-title":"J Mol Biol"},{"key":"ref52","doi-asserted-by":"crossref","first-page":"297","DOI":"10.1006\/jmbi.1996.0794","article-title":"Short-homology-independent illegitimate recombination in <italic>Escherichia coli<\/italic>: distinct mechanism from short-homology-dependent illegitimate recombination.","volume":"266","author":"H Shimizu","year":"1997","journal-title":"J Mol Biol"},{"key":"ref53","doi-asserted-by":"crossref","first-page":"8319","DOI":"10.1073\/pnas.111008398","article-title":"Instability of repetitive DNA sequences: the role of replication in multiple mechanisms.","volume":"98","author":"M Bzymek","year":"2001","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref54","doi-asserted-by":"crossref","first-page":"791","DOI":"10.1016\/j.molcel.2005.07.025","article-title":"A switch from high-fidelity to error-prone DNA double-strand break repair underlies stress-induced mutation.","volume":"19","author":"RG Ponder","year":"2005","journal-title":"Mol Cell"},{"key":"ref55","doi-asserted-by":"crossref","first-page":"e1000175","DOI":"10.1371\/journal.pgen.1000175","article-title":"Segmental duplications arise from Pol32-dependent repair of broken forks through two alternative replication-based mechanisms.","volume":"4","author":"C Payen","year":"2008","journal-title":"PLoS Genet"},{"key":"ref56","doi-asserted-by":"crossref","first-page":"1228","DOI":"10.1016\/j.cell.2007.12.007","article-title":"Template Switching: From Replication Fork Repair to Genome Rearrangements.","volume":"131","author":"D Branzei","year":"2007","journal-title":"Cell"},{"key":"ref57","doi-asserted-by":"crossref","first-page":"10","DOI":"10.1128\/MCB.16.1.10","article-title":"High-frequency illegitimate integration of transfected DNA at preintegrated target sites in a mammalian genome.","volume":"16","author":"RV Merrihew","year":"1996","journal-title":"Mol Cell Biol"},{"key":"ref58","doi-asserted-by":"crossref","first-page":"371","DOI":"10.1093\/genetics\/147.2.371","article-title":"\u201cBreak-copy\u201d duplication: a model for chromosome fragment formation in <italic>Saccharomyces cerevisiae<\/italic>.","volume":"147","author":"DM Morrow","year":"1997","journal-title":"Genetics"},{"key":"ref59","doi-asserted-by":"crossref","first-page":"111","DOI":"10.1146\/annurev.biochem.74.082803.133234","article-title":"Break-Induced Replication and Recombinational Telomere Elongation in Yeast.","volume":"75","author":"MJ McEachern","year":"2006","journal-title":"Annu Rev Biochem"},{"key":"ref60","doi-asserted-by":"crossref","first-page":"102","DOI":"10.1038\/nature05723","article-title":"Template switching during break-induced replication.","volume":"447","author":"CE Smith","year":"2007","journal-title":"Nature"},{"key":"ref61","doi-asserted-by":"crossref","first-page":"820","DOI":"10.1038\/nature06047","article-title":"Break-induced replication and telomerase-independent telomere maintenance require Pol32.","volume":"448","author":"JR Lydeard","year":"2007","journal-title":"Nature"},{"key":"ref62","doi-asserted-by":"crossref","first-page":"2889","DOI":"10.1101\/gad.13.21.2889","article-title":"Double-strand-break repair in <italic>Escherichia coli<\/italic>: physical evidence for a DNA replication mechanism <italic>in vivo<\/italic>.","volume":"13","author":"M Motamedi","year":"1999","journal-title":"Genes Dev"},{"key":"ref63","doi-asserted-by":"crossref","first-page":"859","DOI":"10.4161\/cc.7.7.5613","article-title":"Break-induced replication: what is it and what is it for?","volume":"7","author":"B Llorente","year":"2008","journal-title":"Cell Cycle"},{"key":"ref64","doi-asserted-by":"crossref","first-page":"381","DOI":"10.1016\/0092-8674(85)90152-7","article-title":"Mitotic stability of yeast chromosomes: A colony color assay that measures nondisjunction and chromosome loss.","volume":"40","author":"P Heiter","year":"1985","journal-title":"Cell"},{"key":"ref65","doi-asserted-by":"crossref","first-page":"1845","DOI":"10.1534\/genetics.108.087940","article-title":"Defective break-induced replication leads to half-crossovers in Saccharomyces cerevisiae.","volume":"179","author":"A Deem","year":"2008","journal-title":"Genetics"},{"key":"ref66","doi-asserted-by":"crossref","first-page":"5406","DOI":"10.1128\/MCB.00161-06","article-title":"Control of translocations between highly diverged genes by Sgs1, the Saccharomyces cerevisiae homolog of the Bloom&apos;s syndrome protein.","volume":"26","author":"KH Schmidt","year":"2006","journal-title":"Mol Cell Biol"},{"key":"ref67","doi-asserted-by":"crossref","first-page":"847","DOI":"10.1101\/gr.075903.107","article-title":"Nonrecurrent MECP2 duplications mediated by genomic architecture-driven DNA breaks and break-induced replication repair.","volume":"18","author":"M Bauters","year":"2008","journal-title":"Genome Res"},{"key":"ref68","doi-asserted-by":"crossref","first-page":"851","DOI":"10.1093\/genetics\/160.3.851","article-title":"Crossing over between regions of limited homology in <italic>Escherichia coli<\/italic>. RecA-dependent and RecA-independent pathways.","volume":"160","author":"ST Lovett","year":"2002","journal-title":"Genetics"},{"key":"ref69","doi-asserted-by":"crossref","first-page":"161","DOI":"10.1093\/genetics\/115.1.161","article-title":"Homology requirement for efficient gene conversion between duplicated chromosomal sequences in mammalian cells.","volume":"115","author":"RM Liskay","year":"1987","journal-title":"Genetics"},{"key":"ref70","doi-asserted-by":"crossref","first-page":"1023","DOI":"10.1086\/301827","article-title":"Human meiotic recombination products revealed by sequencing a hotspot for homologous strand exchange in multiple HNPP deletion patients.","volume":"62","author":"LT Reiter","year":"1998","journal-title":"Am J Hum Genet"},{"key":"ref71","doi-asserted-by":"crossref","first-page":"2601","DOI":"10.1128\/MCB.01740-06","article-title":"Inverted DNA repeats channel repair of distant double-strand breaks into chromatid fusions and chromosomal rearrangements.","volume":"27","author":"K VanHulle","year":"2007","journal-title":"Mol Cell Biol"},{"key":"ref72","doi-asserted-by":"crossref","first-page":"2344","DOI":"10.1128\/MCB.24.6.2344-2351.2004","article-title":"RAD51-dependent break-induced replication in yeast.","volume":"24","author":"AP Davis","year":"2004","journal-title":"Mol Cell Biol"},{"key":"ref73","doi-asserted-by":"crossref","first-page":"143","DOI":"10.1093\/genetics\/152.1.143","article-title":"RAD50 and RAD51 define two pathways that collaborate to maintain telomeres in the absence of telomerase.","volume":"152","author":"S Le","year":"1999","journal-title":"Genetics"},{"key":"ref74","doi-asserted-by":"crossref","first-page":"8083","DOI":"10.1128\/MCB.19.12.8083","article-title":"Telomere-telomere recombination is an efficient bypass pathway for telomere maintenance in <italic>Saccharomyces cerevisiae<\/italic>.","volume":"19","author":"SC Teng","year":"1999","journal-title":"Mol Cell Biol"},{"key":"ref75","doi-asserted-by":"crossref","first-page":"5249","DOI":"10.1093\/nar\/gkh842","article-title":"DNA double strand break repair in human bladder cancer is error prone and involves microhomology-associated end-joining.","volume":"32","author":"J Bentley","year":"2004","journal-title":"Nucleic Acids Res"},{"key":"ref76","doi-asserted-by":"crossref","first-page":"483","DOI":"10.1038\/nature06168","article-title":"Rag mutations reveal robust alternative end joining.","volume":"449","author":"B Corneo","year":"2007","journal-title":"Nature"},{"key":"ref77","doi-asserted-by":"crossref","first-page":"699","DOI":"10.1016\/j.cell.2004.08.015","article-title":"Choreography of the DNA damage response: spatiotemporal relationships among checkpoint and repair proteins.","volume":"118","author":"M Lisby","year":"2004","journal-title":"Cell"},{"key":"ref78","doi-asserted-by":"crossref","first-page":"797","DOI":"10.1038\/ng2051","article-title":"Spontaneous DNA breakage in single living cells of <italic>Escherichia coli<\/italic>.","volume":"39","author":"JM Pennington","year":"2007","journal-title":"Nat Gen"},{"key":"ref79","doi-asserted-by":"crossref","first-page":"7158","DOI":"10.1128\/MCB.25.16.7158-7169.2005","article-title":"Spontaneous homologous recombination is induced by collapsed replication forks that are caused by endogenous DNA single-strand breaks.","volume":"25","author":"N Saleh-Gohari","year":"2005","journal-title":"Mol Cell Biol"},{"key":"ref80","doi-asserted-by":"crossref","first-page":"783","DOI":"10.1016\/j.molcel.2005.10.001","article-title":"Human DNA polymerase eta promotes DNA synthesis from strand invasion intermediates of homologous recombination.","volume":"20","author":"MJ McIlwraith","year":"2005","journal-title":"Mol Cell"},{"key":"ref81","doi-asserted-by":"crossref","first-page":"793","DOI":"10.1016\/j.molcel.2005.10.016","article-title":"Dual roles for DNA polymerase eta in homologous DNA recombination and translesion DNA synthesis.","volume":"20","author":"T Kawamoto","year":"2005","journal-title":"Mol Cell"},{"key":"ref82","doi-asserted-by":"crossref","first-page":"11188","DOI":"10.1074\/jbc.M608478200","article-title":"Ability of polymerase eta and T7 DNA polymerase to bypass bulge structures.","volume":"282","author":"VJ Cannistraro","year":"2007","journal-title":"J Biol Chem"},{"key":"ref83","doi-asserted-by":"crossref","first-page":"3049","DOI":"10.1128\/MCB.9.7.3049","article-title":"Comparison of filler DNA at immune, nonimmune, and oncogenic rearrangements suggests multiple mechanisms of formation.","volume":"9","author":"DB Roth","year":"1989","journal-title":"Mol Cell Biol"},{"key":"ref84","doi-asserted-by":"crossref","first-page":"9533","DOI":"10.1073\/pnas.85.24.9533","article-title":"Hypoxia induces DNA overreplication and enhances metastatic potential of murine tumor cells.","volume":"85","author":"SD Young","year":"1988","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref85","doi-asserted-by":"crossref","first-page":"259","DOI":"10.1016\/S1097-2765(00)80137-9","article-title":"A new role for hypoxia in tumor progression: induction of fragile site triggering genomic rearrangements and formation of complex DMs and HSRs.","volume":"2","author":"A Coquelle","year":"1998","journal-title":"Mol Cell"},{"key":"ref86","doi-asserted-by":"crossref","first-page":"237","DOI":"10.1023\/A:1022939318102","article-title":"The hypoxic tumour microenvironment and metastatic progression.","volume":"20","author":"P Subarsky","year":"2003","journal-title":"Clin Exp Metastasis"},{"key":"ref87","doi-asserted-by":"crossref","first-page":"8504","DOI":"10.1128\/MCB.24.19.8504-8518.2004","article-title":"Down-regulation of Rad51 and decreased homologous recombination in hypoxic cancer cells.","volume":"24","author":"RSS Bindra","year":"2004","journal-title":"Mol Cell Biol"},{"key":"ref88","doi-asserted-by":"crossref","first-page":"2048","DOI":"10.1038\/sj.onc.1210001","article-title":"Repression of RAD51 gene expression by E2F4\/p130 complexes in hypoxia.","volume":"26","author":"RS Bindra","year":"2007","journal-title":"Oncogene"},{"key":"ref89","doi-asserted-by":"crossref","first-page":"139","DOI":"10.1007\/s00109-006-0133-6","article-title":"Hypoxia-induced genetic instability\u2013a calculated mechanism underlying tumor progression.","volume":"85","author":"LE Huang","year":"2007","journal-title":"J Mol Med"},{"key":"ref90","doi-asserted-by":"crossref","first-page":"249","DOI":"10.1007\/s10555-007-9061-3","article-title":"Regulation of DNA repair in hypoxic cancer cells.","volume":"26","author":"RS Bindra","year":"2007","journal-title":"Cancer Metastasis Rev"},{"key":"ref91","doi-asserted-by":"crossref","first-page":"699","DOI":"10.1534\/genetics.103.025411","article-title":"Evidence for multiple cycles of strand invasion during repair of double-strand gaps in Drosophila.","volume":"167","author":"M McVey","year":"2004","journal-title":"Genetics"},{"key":"ref92","doi-asserted-by":"crossref","first-page":"93","DOI":"10.1016\/j.canlet.2006.12.011","article-title":"Co-repression of mismatch repair gene expression by hypoxia in cancer cells: role of the Myc\/Max network.","volume":"252","author":"RS Bindra","year":"2007","journal-title":"Cancer Lett"},{"key":"ref93","doi-asserted-by":"crossref","first-page":"3265","DOI":"10.1128\/MCB.23.9.3265-3273.2003","article-title":"Decreased expression of the DNA mismatch repair gene Mlh1 under hypoxic stress in mammalian cells.","volume":"23","author":"VT Mihaylova","year":"2003","journal-title":"Mol Cell Biol"},{"key":"ref94","doi-asserted-by":"crossref","first-page":"1073","DOI":"10.1038\/35082608","article-title":"Multiple pathways cooperate in the suppression of genome instability in Saccharomyces cerevisiae.","volume":"411","author":"K Myung","year":"2001","journal-title":"Nature"},{"key":"ref95","doi-asserted-by":"crossref","first-page":"669","DOI":"10.1534\/genetics.166.2.669","article-title":"General stress response regulator RpoS in adaptive mutation and amplification in <italic>Escherichia coli<\/italic>.","volume":"166","author":"M-J Lombardo","year":"2004","journal-title":"Genetics"},{"key":"ref96","doi-asserted-by":"crossref","first-page":"480","DOI":"10.1126\/science.1411547","article-title":"Removal of nonhomologous DNA ends in double-strand break recombination: the role of the yeast ultraviolet repair gene RAD1.","volume":"258","author":"J Fishman-Lobell","year":"1992","journal-title":"Science"},{"key":"ref97","doi-asserted-by":"crossref","first-page":"10729","DOI":"10.1073\/pnas.93.20.10729","article-title":"DNA strand annealing is promoted by yeast Rad52 protein.","volume":"93","author":"UH Mortensen","year":"1996","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref98","doi-asserted-by":"crossref","first-page":"383","DOI":"10.1093\/genetics\/142.2.383","article-title":"Effects of mutations of RAD50, RAD51, RAD52, and related genes on illegitimate recombination in Saccharomyces cerevisiae.","volume":"142","author":"Y Tsukamoto","year":"1996","journal-title":"Genetics"},{"key":"ref99","doi-asserted-by":"crossref","first-page":"14883","DOI":"10.1074\/jbc.M801097200","article-title":"Rad51 protein controls Rad52-mediated DNA annealing.","volume":"283","author":"Y Wu","year":"2008","journal-title":"J Biol Chem"},{"key":"ref100","doi-asserted-by":"crossref","first-page":"2003","DOI":"10.1534\/genetics.107.076539","article-title":"Saccharomyces cerevisiae Sae2- and Tel1-dependent single-strand DNA formation at DNA break promotes microhomology-mediated end joining.","volume":"176","author":"K Lee","year":"2007","journal-title":"Genetics"},{"key":"ref101","doi-asserted-by":"crossref","first-page":"1182","DOI":"10.1002\/bies.20686","article-title":"An evolution revolution provides further revelation.","volume":"29","author":"JR Lupski","year":"2007","journal-title":"Bioessays"},{"key":"ref102","first-page":"160","article-title":"Evolution by gene duplication","author":"S Ohno","year":"1970"},{"key":"ref103","doi-asserted-by":"crossref","first-page":"e206","DOI":"10.1371\/journal.pbio.0020206","article-title":"Gene duplication: the genomic trade in spare parts.","volume":"2","author":"M Hurles","year":"2004","journal-title":"PLoS Biol"},{"key":"ref104","doi-asserted-by":"crossref","first-page":"677","DOI":"10.1038\/nature06151","article-title":"Gene duplication and the adaptive evolution of a classic genetic switch.","volume":"449","author":"CT Hittinger","year":"2007","journal-title":"Nature"},{"key":"ref105","first-page":"217","article-title":"Uniparental disomy as a mechanism for human genetic disease.","volume":"42","author":"JE Spence","year":"1988","journal-title":"Am J Hum Genet"},{"key":"ref106","doi-asserted-by":"crossref","first-page":"103","DOI":"10.1016\/j.neuron.2006.09.027","article-title":"Genomic rearrangements and gene copy-number alterations as a cause of nervous system disorders.","volume":"52","author":"JA Lee","year":"2006","journal-title":"Neuron"}],"container-title":["PLoS Genetics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pgen.1000327","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,9,30]],"date-time":"2021-09-30T16:38:28Z","timestamp":1633019908000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pgen.1000327"}},"subtitle":[],"editor":[{"given":"Ivan","family":"Matic","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2009,1,30]]},"references-count":106,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2009,1,30]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pgen.1000327","relation":{},"ISSN":["1553-7404"],"issn-type":[{"value":"1553-7404","type":"electronic"}],"subject":[],"published":{"date-parts":[[2009,1,30]]}}}