{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,9,24]],"date-time":"2025-09-24T21:40:20Z","timestamp":1758750020992,"version":"3.44.0"},"reference-count":52,"publisher":"Elsevier","isbn-type":[{"type":"print","value":"9780128139790"}],"license":[{"start":{"date-parts":[[2018,1,1]],"date-time":"2018-01-01T00:00:00Z","timestamp":1514764800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2018,1,1]],"date-time":"2018-01-01T00:00:00Z","timestamp":1514764800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2018,1,1]],"date-time":"2018-01-01T00:00:00Z","timestamp":1514764800000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-017"},{"start":{"date-parts":[[2018,1,1]],"date-time":"2018-01-01T00:00:00Z","timestamp":1514764800000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-037"},{"start":{"date-parts":[[2018,1,1]],"date-time":"2018-01-01T00:00:00Z","timestamp":1514764800000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-012"},{"start":{"date-parts":[[2018,1,1]],"date-time":"2018-01-01T00:00:00Z","timestamp":1514764800000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-029"},{"start":{"date-parts":[[2018,1,1]],"date-time":"2018-01-01T00:00:00Z","timestamp":1514764800000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-004"}],"funder":[{"DOI":"10.13039\/100000090","name":"Congressionally Directed Medical Research Programs","doi-asserted-by":"publisher","award":["BC141727"],"award-info":[{"award-number":["BC141727"]}],"id":[{"id":"10.13039\/100000090","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000054","name":"National Cancer Institute","doi-asserted-by":"publisher","award":["R01ES002614"],"award-info":[{"award-number":["R01ES002614"]}],"id":[{"id":"10.13039\/100000054","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000066","name":"National Institute of Environmental Health Sciences","doi-asserted-by":"publisher","award":["R00ES022633"],"award-info":[{"award-number":["R00ES022633"]}],"id":[{"id":"10.13039\/100000066","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018]]},"DOI":"10.1016\/bs.mie.2017.11.028","type":"book-chapter","created":{"date-parts":[[2018,2,21]],"date-time":"2018-02-21T19:51:06Z","timestamp":1519242666000},"page":"111-144","source":"Crossref","is-referenced-by-count":9,"title":["High-Throughput Analysis of DNA Break-Induced Chromosome Rearrangements by Amplicon Sequencing"],"prefix":"10.1016","member":"78","reference":[{"key":"10.1016\/bs.mie.2017.11.028_bb0010","doi-asserted-by":"crossref","first-page":"169","DOI":"10.1016\/j.dnarep.2014.03.014","article-title":"DNA double-strand break repair pathway choice and cancer","volume":"19","author":"Aparicio","year":"2014","journal-title":"DNA Repair (Amst)"},{"issue":"1\u20134","key":"10.1016\/bs.mie.2017.11.028_bb0015","doi-asserted-by":"crossref","first-page":"92","DOI":"10.1159\/000072843","article-title":"Common fragile sites","volume":"100","author":"Arlt","year":"2003","journal-title":"Cytogenetic and Genome Research"},{"issue":"5","key":"10.1016\/bs.mie.2017.11.028_bb0020","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pgen.1006813","article-title":"Drosophila DNA polymerase theta utilizes both helicase-like and polymerase domains during microhomology-mediated end joining and interstrand crosslink repair","volume":"13","author":"Beagan","year":"2017","journal-title":"PLoS Genetics"},{"issue":"12","key":"10.1016\/bs.mie.2017.11.028_bb0025","doi-asserted-by":"crossref","first-page":"5613","DOI":"10.1073\/pnas.90.12.5613","article-title":"Lethality induced by a single site-specific double-strand break in a dispensable yeast plasmid","volume":"90","author":"Bennett","year":"1993","journal-title":"Proceedings of the National Academy of Sciences of the United States of America"},{"key":"10.1016\/bs.mie.2017.11.028_bb0030","doi-asserted-by":"crossref","first-page":"89","DOI":"10.1111\/nyas.12370","article-title":"Mechanisms of oncogenic chromosomal translocations","volume":"1310","author":"Byrne","year":"2014","journal-title":"Annals of the New York Academy of Sciences"},{"issue":"7","key":"10.1016\/bs.mie.2017.11.028_bb0035","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pgen.1001005","article-title":"Dual roles for DNA polymerase theta in alternative end-joining repair of double-strand breaks in Drosophila","volume":"6","author":"Chan","year":"2010","journal-title":"PLoS Genetics"},{"issue":"1","key":"10.1016\/bs.mie.2017.11.028_bb0040","doi-asserted-by":"crossref","first-page":"107","DOI":"10.1016\/j.cell.2011.07.049","article-title":"Genome-wide translocation sequencing reveals mechanisms of chromosome breaks and rearrangements in B cells","volume":"147","author":"Chiarle","year":"2011","journal-title":"Cell"},{"issue":"51","key":"10.1016\/bs.mie.2017.11.028_bb0045","article-title":"MutS homologue hMSH4: Interaction with eIF3f and a role in NHEJ-mediated DSB repair","volume":"12","author":"Chu","year":"2013","journal-title":"Molecular Cancer"},{"issue":"2","key":"10.1016\/bs.mie.2017.11.028_bb0050","doi-asserted-by":"crossref","first-page":"179","DOI":"10.1016\/j.molcel.2010.09.019","article-title":"The DNA damage response: Making it safe to play with knives","volume":"40","author":"Ciccia","year":"2010","journal-title":"Molecular Cell"},{"issue":"48","key":"10.1016\/bs.mie.2017.11.028_bb0055","article-title":"Alternative end-joining mechanisms: A historical perspective","volume":"4","author":"Decottignies","year":"2013","journal-title":"Frontiers in Genetics"},{"issue":"5910","key":"10.1016\/bs.mie.2017.11.028_bb0060","doi-asserted-by":"crossref","first-page":"133","DOI":"10.1126\/science.1162986","article-title":"Real-time DNA sequencing from single polymerase molecules","volume":"323","author":"Eid","year":"2009","journal-title":"Science"},{"issue":"6","key":"10.1016\/bs.mie.2017.11.028_bb0065","doi-asserted-by":"crossref","first-page":"333","DOI":"10.1038\/nrg.2016.49","article-title":"Coming of age: Ten years of next-generation sequencing technologies","volume":"17","author":"Goodwin","year":"2016","journal-title":"Nature Reviews. Genetics"},{"issue":"49","key":"10.1016\/bs.mie.2017.11.028_bb0070","doi-asserted-by":"crossref","first-page":"42470","DOI":"10.1074\/jbc.M111.309252","article-title":"Correct end use during end joining of multiple chromosomal double strand breaks is influenced by repair protein RAD50, DNA-dependent protein kinase DNA-PKcs, and transcription context","volume":"286","author":"Gunn","year":"2011","journal-title":"The Journal of Biological Chemistry"},{"key":"10.1016\/bs.mie.2017.11.028_bb0075","first-page":"403","article-title":"Physical monitoring of HO-induced homologous recombination","volume":"113","author":"Holmes","year":"1999","journal-title":"Methods in Molecular Biology"},{"key":"10.1016\/bs.mie.2017.11.028_bb0080","first-page":"176","article-title":"Preventing the chromosomal translocations that cause cancer","volume":"127","author":"Hromas","year":"2016","journal-title":"Transactions of the American Clinical and Climatological Association"},{"issue":"3","key":"10.1016\/bs.mie.2017.11.028_bb0085","doi-asserted-by":"crossref","first-page":"214","DOI":"10.1038\/35106058","article-title":"FRA3B and other common fragile sites: The weakest links","volume":"1","author":"Huebner","year":"2001","journal-title":"Nature Reviews. Cancer"},{"issue":"10","key":"10.1016\/bs.mie.2017.11.028_bb0090","doi-asserted-by":"crossref","first-page":"1023","DOI":"10.1016\/j.dnarep.2011.07.011","article-title":"Breadth by depth: Expanding our understanding of the repair of transposon-induced DNA double strand breaks via deep-sequencing","volume":"10","author":"Huefner","year":"2011","journal-title":"DNA Repair (Amst)"},{"issue":"5","key":"10.1016\/bs.mie.2017.11.028_bb0095","doi-asserted-by":"crossref","first-page":"650","DOI":"10.1182\/blood-2016-02-701029","article-title":"XLF deficiency results in reduced N-nucleotide addition during V(D)J recombination","volume":"128","author":"IJspeert","year":"2016","journal-title":"Blood"},{"issue":"1","key":"10.1016\/bs.mie.2017.11.028_bb0100","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/0165-1110(90)90028-A","article-title":"Studies on mammalian mutants defective in rejoining double-strand breaks in DNA","volume":"239","author":"Jeggo","year":"1990","journal-title":"Mutation Research"},{"issue":"3","key":"10.1016\/bs.mie.2017.11.028_bb0105","doi-asserted-by":"crossref","first-page":"230","DOI":"10.1038\/nsmb.2961","article-title":"Mechanism of microhomology-mediated end-joining promoted by human DNA polymerase theta","volume":"22","author":"Kent","year":"2015","journal-title":"Nature Structural & Molecular Biology"},{"issue":"22","key":"10.1016\/bs.mie.2017.11.028_bb0110","doi-asserted-by":"crossref","first-page":"12848","DOI":"10.1093\/nar\/gkx1056","article-title":"Secondary structure forming sequences drive SD-MMEJ repair of DNA double-strand breaks","volume":"45","author":"Khodaverdian","year":"2017","journal-title":"Nucleic Acids Research"},{"issue":"4","key":"10.1016\/bs.mie.2017.11.028_bb0115","doi-asserted-by":"crossref","first-page":"357","DOI":"10.1038\/nmeth.1923","article-title":"Fast gapped-read alignment with Bowtie 2","volume":"9","author":"Langmead","year":"2012","journal-title":"Nature Methods"},{"issue":"4","key":"10.1016\/bs.mie.2017.11.028_bb0120","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":"Lee","year":"2007","journal-title":"Genetics"},{"issue":"14","key":"10.1016\/bs.mie.2017.11.028_bb0125","doi-asserted-by":"crossref","first-page":"1754","DOI":"10.1093\/bioinformatics\/btp324","article-title":"Fast and accurate short read alignment with Burrows-Wheeler transform","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"issue":"16","key":"10.1016\/bs.mie.2017.11.028_bb0130","doi-asserted-by":"crossref","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","article-title":"The sequence alignment\/map format and SAMtools","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"issue":"9","key":"10.1016\/bs.mie.2017.11.028_bb0135","doi-asserted-by":"crossref","first-page":"5172","DOI":"10.1073\/pnas.95.9.5172","article-title":"Homology-directed repair is a major double-strand break repair pathway in mammalian cells","volume":"95","author":"Liang","year":"1998","journal-title":"Proceedings of the National Academy of Sciences of the United States of America"},{"issue":"6","key":"10.1016\/bs.mie.2017.11.028_bb0140","doi-asserted-by":"crossref","first-page":"2769","DOI":"10.1093\/nar\/gkw013","article-title":"Overhang polarity of chromosomal double-strand breaks impacts kinetics and fidelity of yeast non-homologous end joining","volume":"44","author":"Liang","year":"2016","journal-title":"Nucleic Acids Research"},{"key":"10.1016\/bs.mie.2017.11.028_bb0145","doi-asserted-by":"crossref","first-page":"181","DOI":"10.1146\/annurev.biochem.052308.093131","article-title":"The mechanism of double-strand DNA break repair by the nonhomologous DNA end-joining pathway","volume":"79","author":"Lieber","year":"2010","journal-title":"Annual Review of Biochemistry"},{"issue":"12","key":"10.1016\/bs.mie.2017.11.028_bb0150","doi-asserted-by":"crossref","first-page":"8353","DOI":"10.1128\/MCB.19.12.8353","article-title":"Multiple pathways for repair of DNA double-strand breaks in mammalian chromosomes","volume":"19","author":"Lin","year":"1999","journal-title":"Molecular and Cellular Biology"},{"issue":"7538","key":"10.1016\/bs.mie.2017.11.028_bb0155","doi-asserted-by":"crossref","first-page":"254","DOI":"10.1038\/nature14157","article-title":"Mammalian polymerase theta promotes alternative NHEJ and suppresses recombination","volume":"518","author":"Mateos-Gomez","year":"2015","journal-title":"Nature"},{"issue":"5","key":"10.1016\/bs.mie.2017.11.028_bb0160","doi-asserted-by":"crossref","first-page":"2164","DOI":"10.1128\/MCB.16.5.2164","article-title":"Cell cycle and genetic requirements of two pathways of nonhomologous end-joining repair of double-strand breaks in Saccharomyces cerevisiae","volume":"16","author":"Moore","year":"1996","journal-title":"Molecular and Cellular Biology"},{"issue":"17","key":"10.1016\/bs.mie.2017.11.028_bb0165","doi-asserted-by":"crossref","first-page":"8988","DOI":"10.1073\/pnas.94.17.8988","article-title":"Loss of heterozygosity induced by a chromosomal double-strand break","volume":"94","author":"Moynahan","year":"1997","journal-title":"Proceedings of the National Academy of Sciences of the United States of America"},{"issue":"3","key":"10.1016\/bs.mie.2017.11.028_bb0170","doi-asserted-by":"crossref","first-page":"357","DOI":"10.1016\/j.molcel.2005.06.012","article-title":"A gradient of template dependence defines distinct biological roles for family X polymerases in nonhomologous end joining","volume":"19","author":"Nick McElhinny","year":"2005","journal-title":"Molecular Cell"},{"key":"10.1016\/bs.mie.2017.11.028_bb0175","doi-asserted-by":"crossref","first-page":"64","DOI":"10.1016\/j.mrfmmm.2017.07.008","article-title":"Paths from DNA damage and signaling to genome rearrangements via homologous recombination","volume":"806","author":"Nickoloff","year":"2017","journal-title":"Mutation Research"},{"issue":"2","key":"10.1016\/bs.mie.2017.11.028_bb0180","doi-asserted-by":"crossref","first-page":"223","DOI":"10.1016\/j.cell.2007.10.005","article-title":"A backup DNA repair pathway moves to the forefront","volume":"131","author":"Nussenzweig","year":"2007","journal-title":"Cell"},{"issue":"2","key":"10.1016\/bs.mie.2017.11.028_bb0185","doi-asserted-by":"crossref","first-page":"119","DOI":"10.1007\/BF00266917","article-title":"The repair of double-strand breaks in the nuclear DNA of Saccharomyces cerevisiae and its genetic control","volume":"143","author":"Resnick","year":"1976","journal-title":"Molecular & General Genetics"},{"key":"10.1016\/bs.mie.2017.11.028_bb0190","first-page":"4295","article-title":"Nonhomologous recombination in mammalian cells: Role for short sequence homologies in the joining reaction","volume":"6","author":"Roth","year":"1986"},{"issue":"12","key":"10.1016\/bs.mie.2017.11.028_bb0195","first-page":"8096","article-title":"Introduction of double-strand breaks into the genome of mouse cells by expression of a rare-cutting endonuclease","volume":"14","author":"Rouet","year":"1994","journal-title":"Molecular and Cellular Biology"},{"issue":"9","key":"10.1016\/bs.mie.2017.11.028_bb0200","first-page":"3918","article-title":"Efficient repair of HO-induced chromosomal breaks in Saccharomyces cerevisiae by recombination between flanking homologous sequences","volume":"8","author":"Rudin","year":"1988","journal-title":"Molecular and Cellular Biology"},{"key":"10.1016\/bs.mie.2017.11.028_bb0205","series-title":"Mutation Research","article-title":"Microhomology-mediated end joining: Good, bad and ugly","author":"Seol","year":"2017"},{"issue":"11","key":"10.1016\/bs.mie.2017.11.028_bb0210","doi-asserted-by":"crossref","first-page":"701","DOI":"10.1016\/j.tibs.2015.08.006","article-title":"Microhomology-mediated end joining: A back-up survival mechanism or dedicated pathway?","volume":"40","author":"Sfeir","year":"2015","journal-title":"Trends in Biochemical Sciences"},{"key":"10.1016\/bs.mie.2017.11.028_bb0215","doi-asserted-by":"crossref","DOI":"10.1038\/cddis.2015.58","article-title":"Homology and enzymatic requirements of microhomology-dependent alternative end joining","volume":"6","author":"Sharma","year":"2015","journal-title":"Cell Death & Disease"},{"issue":"4","key":"10.1016\/bs.mie.2017.11.028_bb0220","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pgen.1006714","article-title":"Microhomology-mediated end joining induces hypermutagenesis at breakpoint junctions","volume":"13","author":"Sinha","year":"2017","journal-title":"PLoS Genetics"},{"key":"10.1016\/bs.mie.2017.11.028_bb0225","doi-asserted-by":"crossref","first-page":"2","DOI":"10.1016\/j.mrgentox.2015.07.002","article-title":"Marked contribution of alternative end-joining to chromosome-translocation-formation by stochastically induced DNA double-strand-breaks in G2-phase human cells","volume":"793","author":"Soni","year":"2015","journal-title":"Mutation Research, Genetic Toxicology and Environmental Mutagenesis"},{"key":"10.1016\/bs.mie.2017.11.028_bb0230","doi-asserted-by":"crossref","first-page":"44","DOI":"10.1016\/j.dnarep.2014.12.002","article-title":"Development of a novel method to create double-strand break repair fingerprints using next-generation sequencing","volume":"26","author":"Soong","year":"2015","journal-title":"DNA Repair (Amst)"},{"issue":"10","key":"10.1016\/bs.mie.2017.11.028_bb0235","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pgen.1006368","article-title":"Genomic scars generated by polymerase theta reveal the versatile mechanism of alternative end-joining","volume":"12","author":"van Schendel","year":"2016","journal-title":"PLoS Genetics"},{"key":"10.1016\/bs.mie.2017.11.028_bb0240","doi-asserted-by":"crossref","first-page":"175","DOI":"10.1016\/B978-0-12-801185-0.00009-X","article-title":"Assaying break and nick-induced homologous recombination in mammalian cells using the DR-GFP reporter and Cas9 nucleases","volume":"546","author":"Vriend","year":"2014","journal-title":"Methods in Enzymology"},{"issue":"11","key":"10.1016\/bs.mie.2017.11.028_bb0245","doi-asserted-by":"crossref","first-page":"5204","DOI":"10.1093\/nar\/gkw179","article-title":"Distinct genetic control of homologous recombination repair of Cas9-induced double-strand breaks, nicks and paired nicks","volume":"44","author":"Vriend","year":"2016","journal-title":"Nucleic Acids Research"},{"key":"10.1016\/bs.mie.2017.11.028_bb0250","doi-asserted-by":"crossref","first-page":"4286","DOI":"10.1038\/ncomms5286","article-title":"The fidelity of the ligation step determines how ends are resolved during nonhomologous end joining","volume":"5","author":"Waters","year":"2014","journal-title":"Nature Communications"},{"issue":"4","key":"10.1016\/bs.mie.2017.11.028_bb0255","doi-asserted-by":"crossref","first-page":"662","DOI":"10.1016\/j.molcel.2016.06.020","article-title":"Essential roles for polymerase theta-mediated end joining in the repair of chromosome breaks","volume":"63","author":"Wyatt","year":"2016","journal-title":"Molecular Cell"},{"issue":"30","key":"10.1016\/bs.mie.2017.11.028_bb0260","doi-asserted-by":"crossref","first-page":"18545","DOI":"10.1074\/jbc.M115.642884","article-title":"hMSH5 facilitates the repair of camptothecin-induced double-strand breaks through an interaction with FANCJ","volume":"290","author":"Xu","year":"2015","journal-title":"The Journal of Biological Chemistry"},{"issue":"10","key":"10.1016\/bs.mie.2017.11.028_bb0265","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pgen.1004654","article-title":"Mechanism of suppression of chromosomal instability by DNA polymerase POLQ","volume":"10","author":"Yousefzadeh","year":"2014","journal-title":"PLoS Genetics"}],"container-title":["Methods in Enzymology","Mechanisms of DNA Recombination and Genome Rearrangements: Intersection between Homologous Recombination, DNA Replication and DNA Repair"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S007668791730366X?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S007668791730366X?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2025,9,24]],"date-time":"2025-09-24T21:24:42Z","timestamp":1758749082000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S007668791730366X"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2018]]},"ISBN":["9780128139790"],"references-count":52,"URL":"https:\/\/doi.org\/10.1016\/bs.mie.2017.11.028","relation":{},"ISSN":["0076-6879"],"issn-type":[{"type":"print","value":"0076-6879"}],"subject":[],"published":{"date-parts":[[2018]]}}}