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Cellular and genomic approaches for exploring structural chromosomal rearrangements

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Abstract

Human chromosomes are arranged in a linear and conserved sequence order that undergoes further spatial folding within the three-dimensional space of the nucleus. Although structural variations in this organization are an important source of natural genetic diversity, cytogenetic aberrations can also underlie a number of human diseases and disorders. Approaches for studying chromosome structure began half a century ago with karyotyping of Giemsa-banded chromosomes and has now evolved to encompass high-resolution fluorescence microscopy, reporter-based assays, and next-generation DNA sequencing technologies. Here, we provide a general overview of experimental methods at different resolution and sensitivity scales and discuss how they can be complemented to provide synergistic insight into the study of human chromosome structural rearrangements. These approaches range from kilobase-level resolution DNA fluorescence in situ hybridization (FISH)-based imaging approaches of individual cells to genome-wide sequencing strategies that can capture nucleotide-level information from diverse sample types. Technological advances coupled to the combinatorial use of multiple methods have resulted in the discovery of new rearrangement classes along with mechanistic insights into the processes that drive structural alterations in the human genome.

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Abbreviations

BAC:

bacterial artificial chromosome

DNA DSB:

DNA double-strand break

DNA FISH:

DNA fluorescence in situ hybridization

ecDNA:

extrachromosomal DNA

G-banding:

giemsa banding

GCR:

gross chromosomal rearrangement

NOR:

nucleolus organizing region

SIM:

structured illumination microscopy

SNP:

single-nucleotide polymorphism

STORM:

stochastic optical reconstruction microscopy

WGS:

whole-genome sequencing

References

  • Amor DJ, Bentley K, Ryan J, Perry J, Wong L, Slater H, Choo KH (2004) Human centromere repositioning "in progress". Proc Natl Acad Sci U S A 101:6542–6547

    CAS  PubMed  PubMed Central  Google Scholar 

  • Asakawa S, Abe I, Kudoh Y, Kishi N, Wang Y, Kubota R, Kudoh J, Kawasaki K, Minoshima S, Shimizu N (1997) Human BAC library: construction and rapid screening. Gene 191:69–79

    CAS  PubMed  Google Scholar 

  • Baumgartner A, Weier JF, Weier H-UG (2006) Chromosome-specific DNA repeat probes. J Histochem Cytochem 54:1363–1370

    CAS  PubMed  PubMed Central  Google Scholar 

  • Beliveau BJ, Joyce EF, Apostolopoulos N, Yilmaz F, Fonseka CY, McCole R, Chang Y, Li JB, Senaratne TN, Williams BR, Rouillard JM, Wu CT (2012) Versatile design and synthesis platform for visualizing genomes with Oligopaint FISH probes. Proc Natl Acad Sci U S A 109:21301–21306

    CAS  PubMed  PubMed Central  Google Scholar 

  • Beliveau BJ et al (2015) Single-molecule super-resolution imaging of chromosomes and in situ haplotype visualization using Oligopaint FISH probes. Nat Commun 6:7147

    CAS  PubMed  Google Scholar 

  • Beliveau BJ, Boettiger AN, Nir G, Bintu B, Yin P, Zhuang X, Wu CT (2017) In situ super-resolution imaging of genomic DNA with OligoSTORM and OligoDNA-PAINT. Methods Mol Biol 1663:231–252

    CAS  PubMed  PubMed Central  Google Scholar 

  • Beliveau BJ et al (2018) OligoMiner provides a rapid, flexible environment for the design of genome-scale oligonucleotide in situ hybridization probes. Proc Natl Acad Sci 115:E2183–E2192

    CAS  PubMed  PubMed Central  Google Scholar 

  • Ben-David U, Mayshar Y, Benvenisty N (2013) Virtual karyotyping of pluripotent stem cells on the basis of their global gene expression profiles. Nat Protoc 8:989–997

    PubMed  Google Scholar 

  • Bishop R (2010) Applications of fluorescence in situ hybridization (FISH) in detecting genetic aberrations of medical significance. Biosci Horiz 3:85–95

    CAS  Google Scholar 

  • Burman B, Misteli T, Pegoraro G (2015) Quantitative detection of rare interphase chromosome breaks and translocations by high-throughput imaging. Genome Biol 16:146

    PubMed  PubMed Central  Google Scholar 

  • Campbell PJ et al (2008) Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencing. Nat Genet 40:722–729

    CAS  PubMed  PubMed Central  Google Scholar 

  • Chen B, Gilbert LA, Cimini BA, Schnitzbauer J, Zhang W, Li GW, Park J, Blackburn EH, Weissman JS, Qi LS, Huang B (2013) Dynamic imaging of genomic loci in living human cells by an optimized CRISPR/Cas system. Cell 155:1479–1491

    CAS  PubMed  PubMed Central  Google Scholar 

  • Cheung VG, Nowak N, Jang W, Kirsch IR, Zhao S, Chen XN, Furey TS, Kim UJ, Kuo WL, Olivier M, Conroy J, Kasprzyk A, Massa H, Yonescu R, Sait S, Thoreen C, Snijders A, Lemyre E, Bailey JA, Bruzel A, Burrill WD, Clegg SM, Collins S, Dhami P, Friedman C, Han CS, Herrick S, Lee J, Ligon AH, Lowry S, Morley M, Narasimhan S, Osoegawa K, Peng Z, Plajzer-Frick I, Quade BJ, Scott D, Sirotkin K, Thorpe AA, Gray JW, Hudson J, Pinkel D, Ried T, Rowen L, Shen-Ong GL, Strausberg RL, Birney E, Callen DF, Cheng JF, Cox DR, Doggett NA, Carter NP, Eichler EE, Haussler D, Korenberg JR, Morton CC, Albertson D, Schuler G, de Jong PJ, Trask BJ, BAC Resource Consortium (2001) Integration of cytogenetic landmarks into the draft sequence of the human genome. Nature 409:953–958

    CAS  PubMed  PubMed Central  Google Scholar 

  • Chiarle R, Zhang Y, Frock RL, Lewis SM, Molinie B, Ho YJ, Myers DR, Choi VW, Compagno M, Malkin DJ, Neuberg D, Monti S, Giallourakis CC, Gostissa M, Alt FW (2011) Genome-wide translocation sequencing reveals mechanisms of chromosome breaks and rearrangements in B cells. Cell 147:107–119

    CAS  PubMed  PubMed Central  Google Scholar 

  • Chudoba I, Plesch A, Lörch T, Lemke J, Claussen U, Senger G (1999) High resolution multicolor-banding: a new technique for refined FISH analysis of human chromosomes. Cytogenet Cell Genet 84:156–160

    CAS  PubMed  Google Scholar 

  • Crasta K, Ganem NJ, Dagher R, Lantermann AB, Ivanova EV, Pan Y, Nezi L, Protopopov A, Chowdhury D, Pellman D (2012) DNA breaks and chromosome pulverization from errors in mitosis. Nature 482:53–58

    CAS  PubMed  PubMed Central  Google Scholar 

  • Cremer T, Lichter P, Borden J, Ward DC, Manuelidis L (1988) Detection of chromosome aberrations in metaphase and interphase tumor cells by in situ hybridization using chromosome-specific library probes. Hum Genet 80:235–246

    CAS  PubMed  Google Scholar 

  • Dekker J, Rippe K, Dekker M, Kleckner N (2002) Capturing chromosome conformation. Science 295:1306–1311

    CAS  PubMed  Google Scholar 

  • Dixon JR, Xu J, Dileep V, Zhan Y, Song F, le VT, Yardımcı GG, Chakraborty A, Bann DV, Wang Y, Clark R, Zhang L, Yang H, Liu T, Iyyanki S, An L, Pool C, Sasaki T, Rivera-Mulia JC, Ozadam H, Lajoie BR, Kaul R, Buckley M, Lee K, Diegel M, Pezic D, Ernst C, Hadjur S, Odom DT, Stamatoyannopoulos JA, Broach JR, Hardison RC, Ay F, Noble WS, Dekker J, Gilbert DM, Yue F (2018) Integrative detection and analysis of structural variation in cancer genomes. Nat Genet 50:1388–1398

    CAS  PubMed  PubMed Central  Google Scholar 

  • Drets ME, Shaw MW (1971) Specific banding patterns of human chromosomes. Proc Natl Acad Sci U S A 68:2073–2077

    CAS  PubMed  PubMed Central  Google Scholar 

  • Feuk L, Carson AR, Scherer SW (2006) Structural variation in the human genome. Nat Rev Genet 7:85–97

    CAS  PubMed  Google Scholar 

  • Ford CE, Hamerton JL (1956) The chromosomes of man. Nature 178:1020–1023

    CAS  PubMed  Google Scholar 

  • Gall JG, Pardue ML (1969) Formation and detection of RNA-DNA hybrid molecules in cytological preparations. Proc Natl Acad Sci U S A 63:378–383

    CAS  PubMed  PubMed Central  Google Scholar 

  • Genet MD, Cartwright IM, Kato TA (2013) Direct DNA and PNA probe binding to telomeric regions without classical in situ hybridization. Mol Cytogenet 6:42–42

    PubMed  PubMed Central  Google Scholar 

  • Giunta S (2018) Centromere chromosome orientation fluorescent in situ hybridization (Cen-CO-FISH) detects sister chromatid exchange at the centromere in human cells. Bio-protocol 8:e2792

    PubMed  PubMed Central  Google Scholar 

  • Goodpasture C, Bloom SE (1975) Visualization of nucleolar organizer regions im mammalian chromosomes using silver staining. Chromosoma 53:37–50

    CAS  PubMed  Google Scholar 

  • Gustafsson MG et al (2008) Three-dimensional resolution doubling in wide-field fluorescence microscopy by structured illumination. Biophys J 94:4957–4970

    CAS  PubMed  PubMed Central  Google Scholar 

  • Gutiérrez-Mateo C et al (2005) Karyotyping of human oocytes by cenM-FISH, a new 24-colour centromere-specific technique. Hum Reprod 20:3395–3401

    PubMed  Google Scholar 

  • Hausmann M et al (2003) COMBO-FISH: specific labeling of nondenatured chromatin targets by computer-selected DNA oligonucleotide probe combinations. Biotechniques 35(564–570):572–567

    Google Scholar 

  • Hu Q et al (2019) Break-induced replication plays a prominent role in long-range repeat-mediated deletion. EMBO J:e101751

  • Ju YS et al (2015) Frequent somatic transfer of mitochondrial DNA into the nuclear genome of human cancer cells. Genome Res 25:814–824

    CAS  PubMed  PubMed Central  Google Scholar 

  • Kallioniemi A, Kallioniemi OP, Sudar D, Rutovitz D, Gray JW, Waldman F, Pinkel D (1992) Comparative genomic hybridization for molecular cytogenetic analysis of solid tumors. Science 258:818–821

    CAS  PubMed  Google Scholar 

  • Kishi JY, Lapan SW, Beliveau BJ, West ER, Zhu A, Sasaki HM, Saka SK, Wang Y, Cepko CL, Yin P (2019) SABER amplifies FISH: enhanced multiplexed imaging of RNA and DNA in cells and tissues. Nat Methods 16:533–544

    CAS  PubMed  PubMed Central  Google Scholar 

  • Klein IA, Resch W, Jankovic M, Oliveira T, Yamane A, Nakahashi H, di Virgilio M, Bothmer A, Nussenzweig A, Robbiani DF, Casellas R, Nussenzweig MC (2011) Translocation-capture sequencing reveals the extent and nature of chromosomal rearrangements in B lymphocytes. Cell 147:95–106

    CAS  PubMed  PubMed Central  Google Scholar 

  • Kosyakova N et al (2013) Generation of multicolor banding probes for chromosomes of different species. Mol Cytogenet 6:6

    PubMed  PubMed Central  Google Scholar 

  • Le Scouarnec S, Gribble SM (2012) Characterising chromosome rearrangements: recent technical advances in molecular cytogenetics. Heredity (Edinb) 108:75–85

    Google Scholar 

  • Li Y et al (2015) A versatile reporter system for CRISPR-mediated chromosomal rearrangements. Genome Biol 16:111

    PubMed  PubMed Central  Google Scholar 

  • Lichter P, Cremer T, Borden J, Manuelidis L, Ward DC (1988) Delineation of individual human chromosomes in metaphase and interphase cells by in situ suppression hybridization using recombinant DNA libraries. Hum Genet 80:224–234

    CAS  PubMed  Google Scholar 

  • Lieberman-Aiden E, van Berkum N, Williams L, Imakaev M, Ragoczy T, Telling A, Amit I, Lajoie BR, Sabo PJ, Dorschner MO, Sandstrom R, Bernstein B, Bender MA, Groudine M, Gnirke A, Stamatoyannopoulos J, Mirny LA, Lander ES, Dekker J (2009) Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 326:289–293

    CAS  PubMed  PubMed Central  Google Scholar 

  • Lupski JR (1998) Genomic disorders: structural features of the genome can lead to DNA rearrangements and human disease traits. Trends Genet 14:417–422

    CAS  PubMed  Google Scholar 

  • Lupski JR (2007) Genomic rearrangements and sporadic disease. Nat Genet 39:S43–S47

    CAS  PubMed  Google Scholar 

  • Ly P, Teitz LS, Kim DH, Shoshani O, Skaletsky H, Fachinetti D, Page DC, Cleveland DW (2017) Selective Y centromere inactivation triggers chromosome shattering in micronuclei and repair by non-homologous end joining. Nat Cell Biol 19:68–75

    CAS  PubMed  Google Scholar 

  • Ly P, Brunner SF, Shoshani O, Kim DH, Lan W, Pyntikova T, Flanagan AM, Behjati S, Page DC, Campbell PJ, Cleveland DW (2019) Chromosome segregation errors generate a diverse spectrum of simple and complex genomic rearrangements. Nat Genet 51:705–715

    CAS  PubMed  PubMed Central  Google Scholar 

  • Maciejowski J, Li Y, Bosco N, Campbell PJ, de Lange T (2015) Chromothripsis and Kataegis induced by telomere crisis. Cell 163:1641–1654

    CAS  PubMed  PubMed Central  Google Scholar 

  • Mateos-Gomez PA et al (2015) Mammalian polymerase θ promotes alternative NHEJ and suppresses recombination. Nature 518:254

    CAS  PubMed  PubMed Central  Google Scholar 

  • Meltzer PS, Guan XY, Burgess A, Trent JM (1992) Rapid generation of region specific probes by chromosome microdissection and their application. Nat Genet 1:24–28

    CAS  PubMed  Google Scholar 

  • Mendez-Dorantes C, Bhargava R, Stark JM (2018) Repeat-mediated deletions can be induced by a chromosomal break far from a repeat, but multiple pathways suppress such rearrangements. Genes Dev

  • Nathanson DA, Gini B, Mottahedeh J, Visnyei K, Koga T, Gomez G, Eskin A, Hwang K, Wang J, Masui K, Paucar A, Yang H, Ohashi M, Zhu S, Wykosky J, Reed R, Nelson SF, Cloughesy TF, James CD, Rao PN, Kornblum HI, Heath JR, Cavenee WK, Furnari FB, Mischel PS (2014) Targeted therapy resistance mediated by dynamic regulation of extrachromosomal mutant EGFR DNA. Science 343:72–76

    CAS  PubMed  Google Scholar 

  • Nguyen K, Puppo F, Roche S, Gaillard MC, Chaix C, Lagarde A, Pierret M, Vovan C, Olschwang S, Salort-Campana E, Attarian S, Bartoli M, Bernard R, Magdinier F, Levy N (2017) Molecular combing reveals complex 4q35 rearrangements in Facioscapulohumeral dystrophy. Hum Mutat 38:1432–1441

    CAS  PubMed  Google Scholar 

  • Ni Y et al (2017) Super-resolution imaging of a 2.5 kb non-repetitive DNA in situ in the nuclear genome using molecular beacon probes. eLife 6:e21660

    PubMed  PubMed Central  Google Scholar 

  • Nora EP et al (2012) Spatial partitioning of the regulatory landscape of the X-inactivation Centre. Nature 485:381–385

    CAS  PubMed  PubMed Central  Google Scholar 

  • Olsen KE, Knudsen H, Rasmussen BB, Balslev E, Knoop A, Ejlertsen B, Nielsen KV, Schönau A, Overgaard J, Danish Breast Cancer Co-operative Group (2004) Amplification of HER2 and TOP2A and deletion of TOP2A genes in breast cancer investigated by new FISH probes. Acta Oncol 43:35–42

    CAS  PubMed  Google Scholar 

  • Osoegawa K, Mammoser AG, Wu C, Frengen E, Zeng C, Catanese JJ, de Jong PJ (2001) A bacterial artificial chromosome library for sequencing the complete human genome. Genome Res 11:483–496

    CAS  PubMed  PubMed Central  Google Scholar 

  • Pardue ML, Gall JG (1969) Molecular hybridization of radioactive DNA to the DNA of cytological preparations. Proc Natl Acad Sci U S A 64:600–604

    CAS  PubMed  PubMed Central  Google Scholar 

  • Pierce AJ, Johnson RD, Thompson LH, Jasin M (1999) XRCC3 promotes homology-directed repair of DNA damage in mammalian cells. Genes Dev 13:2633–2638

    CAS  PubMed  PubMed Central  Google Scholar 

  • Potapova TA, Unruh JR, Yu Z, Rancati G, Li H, Stampfer MR, Gerton JL (2019) Superresolution microscopy reveals linkages between ribosomal DNA on heterologous chromosomes. J Cell Biol 218:2492–2513

    PubMed  PubMed Central  Google Scholar 

  • Raap AK, Florijn RJ, Blonden LAJ, Wiegant J, Vaandrager JW, Vrolijk H, den Dunnen J, Tanke HJ, van Ommen G (1996) Fiber FISH as a DNA mapping tool. Methods 9:67–73

    CAS  PubMed  Google Scholar 

  • Ried T, Schröck E, Ning Y, Wienberg J (1998) Chromosome painting: a useful art. Hum Mol Genet 7:1619–1626

    CAS  PubMed  Google Scholar 

  • Roix JJ, McQueen PG, Munson PJ, Parada LA, Misteli T (2003) Spatial proximity of translocation-prone gene loci in human lymphomas. Nat Genet 34:287–291

    CAS  PubMed  Google Scholar 

  • Roschke A, Ning Y, Smith ACM, Macha M, Precht K, Riethman H, Ledbetter DH, Flint J, Horsley S, Regan R, Kearney L, Knight S, Kvaloy K, Brown WRA (1996) A complete set of human telomeric probes and their clinical application. National Institutes of Health and Institute of Molecular Medicine collaboration. Nat Genet 14:86–89

    Google Scholar 

  • Roukos V, Voss TC, Schmidt CK, Lee S, Wangsa D, Misteli T (2013) Spatial dynamics of chromosome translocations in living cells. Science 341:660–664

    CAS  PubMed  PubMed Central  Google Scholar 

  • Roukos V, Burgess RC, Misteli T (2014) Generation of cell-based systems to visualize chromosome damage and translocations in living cells. Nat Protoc 9:2476–2492

    CAS  PubMed  PubMed Central  Google Scholar 

  • Rowley JD (1973) A new consistent chromosomal abnormality in chronic myelogenous leukaemia identified by quinacrine fluorescence and Giemsa staining. Nature 243:290–293

    CAS  PubMed  Google Scholar 

  • Rudin CM, Durinck S, Stawiski EW, Poirier JT, Modrusan Z, Shames DS, Bergbower EA, Guan Y, Shin J, Guillory J, Rivers CS, Foo CK, Bhatt D, Stinson J, Gnad F, Haverty PM, Gentleman R, Chaudhuri S, Janakiraman V, Jaiswal BS, Parikh C, Yuan W, Zhang Z, Koeppen H, Wu TD, Stern HM, Yauch RL, Huffman KE, Paskulin DD, Illei PB, Varella-Garcia M, Gazdar AF, de Sauvage FJ, Bourgon R, Minna JD, Brock MV, Seshagiri S (2012) Comprehensive genomic analysis identifies SOX2 as a frequently amplified gene in small-cell lung cancer. Nat Genet 44:1111–1116

    CAS  PubMed  PubMed Central  Google Scholar 

  • Rudkin GT, Stollar BD (1977) High resolution detection of DNA-RNA hybrids in situ by indirect immunofluorescence. Nature 265:472–473

    CAS  PubMed  Google Scholar 

  • Rust MJ, Bates M, Zhuang X (2006) Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM). Nat Methods 3:793–795

    CAS  PubMed  PubMed Central  Google Scholar 

  • Schnedl W (1971) Banding pattern of human chromosomes. Nat New Biol 233:93–94

    CAS  PubMed  Google Scholar 

  • Schrock E et al (1996) Multicolor spectral karyotyping of human chromosomes. Science 273:494–497

    CAS  PubMed  Google Scholar 

  • Seabright M (1971) A rapid banding technique for human chromosomes. Lancet 2:971–972

    CAS  PubMed  Google Scholar 

  • Shizuya H, Birren B, Kim UJ, Mancino V, Slepak T, Tachiiri Y, Simon M (1992) Cloning and stable maintenance of 300-kilobase-pair fragments of human DNA in Escherichia coli using an F-factor-based vector. Proc Natl Acad Sci U S A 89:8794–8797

    CAS  PubMed  PubMed Central  Google Scholar 

  • Solinas-Toldo S, Lampel S, Stilgenbauer S, Nickolenko J, Benner A, Döhner H, Cremer T, Lichter P (1997) Matrix-based comparative genomic hybridization: biochips to screen for genomic imbalances. Genes Chromosomes Cancer 20:399–407

    CAS  PubMed  Google Scholar 

  • Speicher MR, Carter NP (2005) The new cytogenetics: blurring the boundaries with molecular biology. Nat Rev Genet 6:782–792

    CAS  PubMed  Google Scholar 

  • Speicher MR, Gwyn Ballard S, Ward DC (1996) Karyotyping human chromosomes by combinatorial multi-fluor FISH. Nat Genet 12:368–375

    CAS  PubMed  Google Scholar 

  • Steinhaeuser U, Starke H, Nietzel A, Lindenau J, Ullmann P, Claussen U, Liehr T (2002) Suspension (S)-FISH, a new technique for interphase nuclei. J Histochem Cytochem 50:1697–1698

    CAS  PubMed  Google Scholar 

  • Stephens PJ, Greenman CD, Fu B, Yang F, Bignell GR, Mudie LJ, Pleasance ED, Lau KW, Beare D, Stebbings LA, McLaren S, Lin ML, McBride D, Varela I, Nik-Zainal S, Leroy C, Jia M, Menzies A, Butler AP, Teague JW, Quail MA, Burton J, Swerdlow H, Carter NP, Morsberger LA, Iacobuzio-Donahue C, Follows GA, Green AR, Flanagan AM, Stratton MR, Futreal PA, Campbell PJ (2011) Massive genomic rearrangement acquired in a single catastrophic event during cancer development. Cell 144:27–40

    CAS  PubMed  PubMed Central  Google Scholar 

  • Sugita S, Hasegawa T (2017) Practical use and utility of fluorescence in situ hybridization in the pathological diagnosis of soft tissue and bone tumors. J Orthop Sci 22:601–612

    PubMed  Google Scholar 

  • Sumner AT, Evans HJ, Buckland RA (1971) New technique for distinguishing between human chromosomes. Nat New Biol 232:31–32

    CAS  PubMed  Google Scholar 

  • Telenius H, Carter NP, Bebb CE, Nordenskjöld M, Ponder BA, Tunnacliffe A (1992) Degenerate oligonucleotide-primed PCR: general amplification of target DNA by a single degenerate primer. Genomics 13:718–725

    CAS  PubMed  Google Scholar 

  • Tjio JH, Levan A (1956) The Chromosome Number of Man. Hereditas 42:1–6

    Google Scholar 

  • Tkachuk DC, Westbrook CA, Andreeff M, Donlon TA, Cleary ML, Suryanarayan K, Homge M, Redner A, Gray J, Pinkel D (1990) Detection of bcr-abl fusion in chronic myelogeneous leukemia by in situ hybridization. Science 250:559–562

    CAS  PubMed  Google Scholar 

  • Tosuji H, Mabuchi I, Fusetani N, Nakazawa T (1992) Calyculin a induces contractile ring-like apparatus formation and condensation of chromosomes in unfertilized sea urchin eggs. Proc Natl Acad Sci U S A 89:10613–10617

    CAS  PubMed  PubMed Central  Google Scholar 

  • Trask BJ (2002) Human cytogenetics: 46 chromosomes, 46 years and counting. Nat Rev Genet 3:769–778

    CAS  PubMed  Google Scholar 

  • Turner KM, Deshpande V, Beyter D, Koga T, Rusert J, Lee C, Li B, Arden K, Ren B, Nathanson DA, Kornblum HI, Taylor MD, Kaushal S, Cavenee WK, Wechsler-Reya R, Furnari FB, Vandenberg SR, Rao PN, Wahl GM, Bafna V, Mischel PS (2017) Extrachromosomal oncogene amplification drives tumour evolution and genetic heterogeneity. Nature 543:122–125

    CAS  PubMed  PubMed Central  Google Scholar 

  • van der Burg M, Poulsen TS, Hunger SP, Beverloo HB, Smit EM, Vang-Nielsen K, Langerak AW, van Dongen J (2004) Split-signal FISH for detection of chromosome aberrations in acute lymphoblastic leukemia. Leukemia 18:895–908

    PubMed  Google Scholar 

  • Veldman T, Vignon C, Schrock E, Rowley JD, Ried T (1997) Hidden chromosome abnormalities in haematological malignancies detected by multicolour spectral karyotyping. Nat Genet 15:406–410

    CAS  PubMed  Google Scholar 

  • Verhaak RGW, Bafna V, Mischel PS (2019) Extrachromosomal oncogene amplification in tumour pathogenesis and evolution. Nat Rev Cancer 19:283–288

    CAS  PubMed  PubMed Central  Google Scholar 

  • Vorsanova SG, Yurov YB, Iourov IY (2010) Human interphase chromosomes: a review of available molecular cytogenetic technologies. Mol Cytogenet 3:1

    PubMed  PubMed Central  Google Scholar 

  • Wang DG, Fan JB, Siao CJ, Berno A, Young P, Sapolsky R, Ghandour G, Perkins N, Winchester E, Spencer J, Kruglyak L, Stein L, Hsie L, Topaloglou T, Hubbell E, Robinson E, Mittmann M, Morris MS, Shen N, Kilburn D, Rioux J, Nusbaum C, Rozen S, Hudson TJ, Lipshutz R, Chee M, Lander ES (1998) Large-scale identification, mapping, and genotyping of single-nucleotide polymorphisms in the human genome. Science 280:1077–1082

    CAS  PubMed  Google Scholar 

  • Wang H et al. (2019) CRISPR-mediated live imaging of genome editing and transcription. Science

  • Weier H-UG (2001) DNA Fiber mapping techniques for the assembly of high-resolution physical maps. J Histochem Cytochem 49:939–948

    CAS  PubMed  Google Scholar 

  • Weinstock DM, Elliott B, Jasin M (2006) A model of oncogenic rearrangements: differences between chromosomal translocation mechanisms and simple double-strand break repair. Blood 107:777–780

    CAS  PubMed  PubMed Central  Google Scholar 

  • Yunis JJ, Roldan L, Yasmineh WG, Lee JC (1971) Staining of satellite DNA in metaphase chromosomes. Nature 231:532–533

    CAS  PubMed  Google Scholar 

  • Zhang Y, McCord R, Ho YJ, Lajoie BR, Hildebrand DG, Simon AC, Becker MS, Alt FW, Dekker J (2012) Spatial organization of the mouse genome and its role in recurrent chromosomal translocations. Cell 148:908–921

    CAS  PubMed  PubMed Central  Google Scholar 

  • Zhang CZ, Spektor A, Cornils H, Francis JM, Jackson EK, Liu S, Meyerson M, Pellman D (2015) Chromothripsis from DNA damage in micronuclei. Nature 522:179–184

    CAS  PubMed  PubMed Central  Google Scholar 

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Acknowledgments

We thank Kathleen Wilson and Sangeeta Patel (UT Southwestern Medical Center) for providing figures of G-banded karyotypes. This work was supported by the US National Institutes of Health (R00CA218871 to P.L.) and the Cancer Prevention and Research Institute of Texas (RR180050 to P.L.).

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  1. Department of Pathology, Department of Cell Biology, Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA

    Qing Hu, Elizabeth G. Maurais & Peter Ly

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Hu, Q., Maurais, E.G. & Ly, P. Cellular and genomic approaches for exploring structural chromosomal rearrangements. Chromosome Res 28, 19–30 (2020). https://doi.org/10.1007/s10577-020-09626-1

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