Benner, SE, Wahl, GM & Von Hoff, DD Double-minute chromosomes and regions of homogeneous staining in tumors taken directly from patients versus in human tumor cell lines. Anticancer Medicines two, 11-25 (1991).
Turner, KM et al. Amplification of the extrachromosomal oncogene drives tumor evolution and genetic heterogeneity. Nature 543, 122-125 (2017).
Albertson, DG Gene amplification in cancer. Trends Genet. 22, 447–455 (2006).
Alt, FW, Kellems, RE, Bertino, JR & Schimke, RT Selective multiplication of dihydrofolate reductase genes in methotrexate resistant variants of murine cells in culture. J. Biol. Chem. 253, 1357–1370 (1978).
Kaufman, RJ, Brown, PC & Schimke, RT Dihydrofolate reductase genes amplified in unstable methotrexate resistant cells are associated with double-minute chromosomes. Proc. Natl Acad. Sci. USA 76, 5669–5673 (1979).
Nunberg, JH, Kaufman, RJ, Schimke, RT, Urlaub, G. & Chasin, LA The amplified dihydrofolate reductase genes are located in a region of homogeneous staining of a single chromosome in a Chinese hamster ovary cell line resistant to methotrexate. Proc. Natl Acad. Sci. USA 75, 5553–5556 (1978).
Carroll, SM et al. Double-minute chromosomes can be produced from precursors derived from a chromosomal deletion. Mol. Cell. Biol. 8, 1525–1533 (1988).
Ruiz, JC & Wahl, GM Chromosomal destabilization during gene amplification. Mol. Cell. Biol. 10, 3056-3066 (1990).
Coquelle, A., Rozier, L., Dutrillaux, B. & Debatisse, M. The induction of multiple double strand breaks within an hsr by meganucleaseI-SceI expression or fragile site activation leads to the formation of double and other minutes chromosomal rearrangements. Oncogene 21, 7671-7679 (2002).
Nathanson, DA et al. Resistance to targeted therapy mediated by dynamic regulation of EGFR extrachromosomal mutant DNA. Science 343, 72-76 (2014).
The ICGC / TCGA Pan-Cancer Analysis Consortium for Whole Genomes. Pan-cancerous analysis of whole genomes. Nature 578, 82-93 (2020).
Li, Y. et al. Patterns of somatic structural variation in human cancer genomes. Nature 578, 112-121 (2020).
Cortes-Ciriano, I. et al. Comprehensive analysis of chromotripsy in 2,658 human cancers using complete genome sequencing. Nat. Genet. 52, 331–341 (2020).
Stephens, PJ et al. Massive genomic reorganization acquired in a single catastrophic event during the development of cancer. Cell 144, 27–40 (2011).
deCarvalho, AC et al. The discordant inheritance of chromosomal and extrachromosomal DNA elements contributes to the dynamic evolution of the disease in glioblastoma. Nat. Genet. 50, 708-717 (2018).
Verhaak, RGW, Bafna, V. & Mischel, PS Extrachromosomal oncogene amplification in tumor pathogenesis and evolution. Nat. Rev. Cancer 19, 283–288 (2019).
Rausch, T. et al. The sequencing of the pediatric medulloblastoma genome links catastrophic DNA rearrangements with mutations in TP53. Cell 148, 59–71 (2012).
Nones, K. et al. Genomic catastrophes often arise in esophageal adenocarcinoma and lead to tumorigenesis. Common Nat.. 5, 5224 (2014).
Ly, P. et al. Chromosomal segregation errors generate a diverse spectrum of simple and complex genomic rearrangements. Nat. Genet. 51, 705–715 (2019).
Singer, MJ, Mesner, LD, Friedman, CL, Trask, BJ & Hamlin, JL The amplification of the human dihydrofolate reductase gene through double minutes is initiated by chromosomal breaks. Proc. Natl Acad. Sci. USA 97, 7921-7926 (2000).
Windle, B., Draper, BW, Yin, YX, O’Gorman, S. & Wahl, GM A central role for the chromosome break in gene amplification, deletion formation and amplicon integration. Dev genes. 5, 160-174 (1991).
McClintock, B. The stability of the broken ends of chromosomes in Zea mays. Genetics 26, 234–282 (1941).
Glodzik, D. et al. A somatic mutational process repeatedly duplicates the germ line susceptibility loci and the tissue-specific super enhancers in breast cancers. Nat. Genet. 49, 341–348 (2017).
Garsed, DW et al. The architecture and evolution of cancer neochromosomes. Cancer cell 26, 653–667 (2014).
Landry, JJ et al. The genomic and transcriptomic landscape of a HeLa cell line. G3 (Bethesda) 3, 1213–1224 (2013).
Zhang, CZ et al. Chromotripsy of DNA damage in micronuclei. Nature 522, 179-184 (2015).
Yaeger, R. et al. The mechanisms of acquired resistance to BRAF V600E inhibition in colon cancers converge to RAF dimerization and are sensitive to its inhibition. Cancer Res. 77, 6513–6523 (2017).
Ly, P. et al. The selective inactivation of the Y centromere triggers chromosomal fragmentation in micronuclei and repair by non-homologous end junction. Nat. Cell Biol. 19, 68-75 (2017).
Shimizu, N., Hashizume, T., Shingaki, K. & Kawamoto, JK Amplification of plasmids containing a mammalian replication initiation region is mediated by a controllable conflict between replication and transcription. Cancer Res. 63, 5281–5290 (2003).
Maciejowski, J., Li, Y., Bosco, N., Campbell, PJ & de Lange, T. Chromothripsis and kataegis induced by telomere crisis. Cell 163, 1641–1654 (2015).
Hoffelder, DR et al. Resolution of anaphase bridges in cancer cells. Chromosome 112, 389-397 (2004).
Heltay, T., Petermann, E., Lundin, C., Hodgson, B. & Sharma, RA DNA repairways as targets for cancer therapy. Nat. Rev. Cancer 8, 193–204 (2008).
Cermak, T. et al. Efficient design and assembly of customized TALEN and other constructions based on TAL effectors for targeting DNA. Nucleic acid res. 39, e82 (2011).
Fachinetti, D. et al. The specific binding of the CENP-B DNA sequence increases the fidelity of the human centromere function. Dev. Cell 33, 314-327 (2015).
Schindelin, J. et al. Fiji: an open source platform for analyzing biological images. Nat. Methods 9, 676–682 (2012).
Or, HD et al. ChromEMT: visualization of the structure and compaction of 3D chromatin in interphase and mitotic cells. Science 357, eaag0025 (2017).
Or, HD, Deerinck, TJ, Bushong, E., Ellisman, MH & O’Shea, CC Visualizing viral protein structures in cells using genetic probes for light microscopy and correlated electronics. Methods 90, 39–48 (2015).
Rao, SS et al. A 3D map of the human genome with kilobase resolution reveals the principles of the chromatin loop. Cell 159, 1665-1680 (2014).
Li, H. & Durbin, R. Fast and accurate long reading alignment with Burrows-Wheeler transform. Bioinformatics 26, 589–595 (2010).
Raine, KM et al. ascatNgs: identify changes in the number of copies acquired somatically from sequencing data of the entire genome. Curr. Protoc. Bioinformatics 56, 15.9.1– 15.9.17 (2016).
Nik-Zainal, S. et al. Landscape of somatic mutations in 560 sequences of the total breast cancer genome. Nature 534, 47–54 (2016).
Korbel, JO & Campbell, PJ Criteria for inference of chromothripsis in cancer genomes. Cell 152, 1226–1236 (2013).
Li, Y. et al. Constitutional and somatic rearrangement of chromosome 21 in acute lymphoblastic leukemia. Nature 508, 98-102 (2014).
Alexandrov, LB, Nik-Zainal, S., Wedge, DC, Campbell, PJ & Stratton, MR Deciphering signatures of mutational processing operative in human cancer. Cell Rep. 3, 246-259 (2013).