How to count chromosomes in a cell: An overview of current and novel technologies

BioEssays

Volumn 37, Issue 5, 2015, Pages 570-577

  Bakker, Bjorn ^a   van den Bos, Hilda ^a   Lansdorp, Peter M ^a   Foijer, Floris ^a  

^a UNIVERSITY MEDICAL CENTER GRONINGEN   (Netherlands)

Author keywords

Aneuploidy; Chromosomal instability; Karyotyping; Next generation sequencing

Indexed keywords

ANEUPLOIDY; ARTICLE; CANCER CELL; CELL POPULATION; CHROMOSOME NUMBER; COMPARATIVE GENOMIC HYBRIDIZATION; FLOW CYTOMETRY; FLUORESCENCE IN SITU HYBRIDIZATION; GENE DOSAGE; GENETIC HETEROGENEITY; INTERPHASE; KARYOTYPING; METAPHASE CHROMOSOME; NERVE DEGENERATION; NEXT GENERATION SEQUENCING; SINGLE CELL ANALYSIS; SINGLE NUCLEOTIDE POLYMORPHISM; SPECTRAL KARYOTYPING; ANIMAL; CHROMOSOMAL INSTABILITY; CHROMOSOME; GENETICS; HIGH THROUGHPUT SEQUENCING; HUMAN;

ANEUPLOIDY; ANIMALS; CHROMOSOMAL INSTABILITY; CHROMOSOMES; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; KARYOTYPING;

EID: 84927911075     PISSN: 02659247     EISSN: 15211878     Source Type: Journal    
DOI: 10.1002/bies.201400218     Document Type: Article

References (77)

1. Boveri T, Manchester KL. 1995. Theodor Boveri-the origin of malignant tumours. Trends Cell Biol 5: 384-7.
2. Bignold LP, Coghlan BLD, Jersmann HP. 2006. Hansemann, Boveri, chromosomes and the gametogenesis-related theories of tumours. Cell Biol Int 30: 640-4.
3. Boveri T. 2008. Concerning the origin of malignant tumours by Theodor Boveri. Translated and annotated by Henry Harris. J Cell Sci 121: 1-84.
4. Neri G, Opitz JM. 2009. Down syndrome: comments and reflections on the 50th anniversary of Lejeune's discovery. Am J Med Genet A 149A: 2647-54.
5. Patau K, Smith D, Therman E, Inhorn S, et al. 1960. Multiple congenital anomaly caused by an extra autosome. Lancet 275: 790-3.
6. Edwards J, Harnden D, Cameron A, Mary Crosse V, et al. 1960. A new trisomic syndrome. Lancet 275: 787-90.
7. Duijf PHG, Benezra R. 2013. The cancer biology of whole-chromosome instability. Oncogene 32: 4727-36.
8. Duijf PHG, Schultz N, Benezra R. 2013. Cancer cells preferentially lose small chromosomes. Int J Cancer 132: 2316-26.
9. Weaver BAA, Cleveland DW. 2006. Does aneuploidy cause cancer? Curr Opin Cell Biol 18: 658-67.
10. Hanahan D, Weinberg RA. 2011. Hallmarks of cancer: the next generation. Cell 144: 646-74.
11. Torres EM, Williams BR, Amon A. 2008. Aneuploidy: cells losing their balance. Genetics 179: 737-46.
12. Pfau SJ, Amon A. 2012. Chromosomal instability and aneuploidy in cancer: from yeast to man. EMBO Rep 13: 515-27.
13. Torres EM, Sokolsky T, Tucker CM, Chan LY, et al. 2007. Effects of aneuploidy on cellular physiology and cell division in haploid yeast. Science 317: 916-24.
14. Sheltzer JM, Amon A. 2011. The aneuploidy paradox: costs and benefits of an incorrect karyotype. Trends Genet 27: 446-53.
15. Gordon DJ, Resio B, Pellman D. 2012. Causes and consequences of aneuploidy in cancer. Nat Rev Genet 13: 189-203.
16. Musacchio A, Salmon ED. 2007. The spindle-assembly checkpoint in space and time. Mol Cell 8: 379-93.
17. Hanks S, Coleman K, Summersgill B, Messahel B, et al. 2006. Comparative genomic hybridization and BUB1B mutation analyses in childhood cancers associated with mosaic variegated aneuploidy syndrome. Cancer Lett 239: 234-8.
18. Hanks S, Coleman K, Reid S, Plaja A, et al. 2004. Constitutional aneuploidy and cancer predisposition caused by biallelic mutations in BUB1B. Nat Genet 36: 1159-61.
19. Schvartzman J-M, Sotillo R, Benezra R. 2010. Mitotic chromosomal instability and cancer: mouse modelling of the human disease. Nat Rev Cancer 10: 102-15.
20. Holland AJ, Cleveland DW. 2009. Boveri revisited: chromosomal instability, aneuploidy and tumorigenesis. Nat Rev Mol Cell Biol 10: 478-87.
21. Foijer F, Draviam VM, Sorger PK. 2008. Studying chromosome instability in the mouse. Biochim Biophys Acta 1786: 73-82.
22. Foijer F, DiTommaso T, Donati G, Hautaviita K, et al. 2013. Spindle checkpoint deficiency is tolerated by murine epidermal cells but not hair follicle stem cells. Proc Natl Acad Sci USA 110: 2928-33.
23. Yurov YB, Iourov IY, Monakhov VV, Soloviev IV, et al. 2005. The variation of aneuploidy frequency in the developing and adult human brain revealed by an interphase FISH study. J Histochem Cytochem 53: 385-90.
24. Mosch B, Morawski M, Mittag A, Lenz D, et al. 2007. Aneuploidy and DNA replication in the normal human brain and Alzheimer's disease. J Neurosci 27: 6859-67.
25. Westra JW, Peterson SE, Yung YC, Mutoh T, et al. 2008. Aneuploid mosaicism in the developing and adult cerebellar cortex. J Comp Neurol 507: 1944-51.
26. Pack SD, Weil RJ, Vortmeyer AO, Zeng W, et al. 2014. Individual adult human neurons display aneuploidy: Detection by fluorescence in situ hybridization and single neuron PCR. Cell Cycle 4: 1758-60.
27. Kingsbury M, Friedman B, McConnell M, Rehen S, et al. 2005. Aneuploid neurons are functionally active and integrated into brain circuitry. Proc Natl Acad Sci USA 102: 6143-7.
28. Knouse KA, Wu J, Whittaker CA, Amon A. 2014. Single cell sequencing reveals low levels of aneuploidy across mammalian tissues. Proc Natl Acad Sci USA 111: 13409-14.
29. Iourov IY, Vorsanova SG, Liehr T, Yurov YB. 2009. Aneuploidy in the normal, Alzheimer's disease and ataxia-telangiectasia brain: differential expression and pathological meaning. Neurobiol Dis 34: 212-20.
30. Yurov YB, Vorsanova SG, Iourov IY. 2009. GIN'n'CIN hypothesis of brain aging: deciphering the role of somatic genetic instabilities and neural aneuploidy during ontogeny. Mol Cytogenet 2: 23.
31. Thomas P, Fenech M. 2008. Chromosome 17 and 21 aneuploidy in buccal cells is increased with ageing and in Alzheimer's disease. Mutagenesis 23: 57-65.
32. Yurov YB, Vorsanova SG, Liehr T, Kolotii AD, et al. 2014. X chromosome aneuploidy in the Alzheimer's disease brain. Mol Cytogenet 7: 20.
33. Mitchison TJ. 2012. The proliferation rate paradox in antimitotic chemotherapy. Mol Biol Cell 23: 1-6.
34. Das K, Tan P. 2013. Molecular cytogenetics: recent developments and applications in cancer. Clin Genet 84: 315-25.
35. McGranahan N, Burrell RA, Endesfelder D, Novelli MR, et al. 2012. Cancer chromosomal instability: therapeutic and diagnostic challenges. EMBO Rep 13: 528-38.
36. Pellestor F, Anahory T, Hamamah S. 2005. The chromosomal analysis of human oocytes. An overview of established procedures. Hum Reprod Update 11: 15-32.
37. Bayani J, Squire J. 2004. Multi-color FISH techniques. Curr Protoc Cell Biol Chapter 22: Unit 22.5.
38. Liehr T, Starke H, Weise A, Lehrer H, et al. 2004. Multicolor FISH probe sets and their applications. Histol Histopathol 19: 229-37.
39. Bayani JM, Squire JA. 2002. Applications of SKY in cancer cytogenetics. Cancer Invest 20: 373-86.
40. Padilla-Nash HM, Barenboim-Stapleton L, Difilippantonio MJ, Ried T. 2006. Spectral karyotyping analysis of human and mouse chromosomes. Nat Protoc 1: 3129-42.
41. Speicher MR, Carter NP. 2005. The new cytogenetics: blurring the boundaries with molecular biology. Nat Rev Genet 6: 782-92.
42. Imataka G, Arisaka O. 2012. Chromosome analysis using spectral karyotyping (SKY). Cell Biochem Biophys 62: 13-7.
43. Jiang J, Gill BS. 2006. Current status and the future of fluorescence in situ hybridization (FISH) in plant genome research. Genome 49: 1057-68.
44. Szuhai K, Tanke HJ. 2006. COBRA: combined binary ratio labeling of nucleic- acid probes for multi-color fluorescence in situ hybridization karyotyping. Nat Protoc 1: 264-75.
45. Szuhai K, Bezrookove V, Wiegant J, Vrolijk J, et al. 2000. Simultaneous Molecular Karyotyping and Mapping of Viral DNA Integration Sites by 25-Color COBRA-FISH. Genes Chromosomes Cancer 97: 92-7.
46. Kuźniacka A, Mertens F, Strömbeck B, Wiegant J, et al. 2004. Combined binary ratio labeling fluorescence in situ hybridization analysis of chordoma. Cancer Genet Cytogenet 151: 178-81.
47. Liehr T, Heller A, Starke H, Rubtsov N, et al. 2002. Microdissection based high resolution multicolor banding for all 24 human chromosomes. Int J Mol Med 9: 335-9.
48. Williams BR, Prabhu VR, Hunter KE, Glazier CM, et al. 2008. Aneuploidy affects proliferation and spontaneous immortalization in mammalian cells. Science 322: 703-9.
49. Foijer F, Xie SZ, Simon JE, Bakker PL, et al. 2014. Chromosome instability induced by Mps1 and p53 mutation generates aggressive lymphomas exhibiting aneuploidy-induced stress. Proc Natl Acad Sci USA 111: 13427-32.
50. Tribukait B, Granberg-Ohman I, Wijkström H. 1986. Flow cytometric DNA and cytogenetic studies in human tumors: a comparison and discussion of the differences in modal values obtained by the two methods. Cytometry 7: 194-9.
51. Doležel J, Vrána J, Safář J, Bartoš J, et al. 2012. Chromosomes in the flow to simplify genome analysis. Funct Integr Genomics 12: 397-416.
52. Weiss MM, Hermsen MA, Meijer GA, van Grieken NC, et al. 1999. Comparative genomic hybridisation. Mol Pathol 52: 243-51.
53. Oostlander A, Meijer G, Ylstra B. 2004. Microarray-based comparative genomic hybridization and its applications in human genetics. Clin Genet 66: 488-95.
54. Brady PD, Vermeesch JR. 2012. Genomic microarrays: a technology overview. Prenat Diagn 32: 336-43.
55. Kallioniemi A. 2008. CGH microarrays and cancer. Curr Opin Biotechnol 19: 36-40.
56. Bignell GR, Huang J, Greshock J, Watt S, et al. 2004. High-resolution analysis of DNA copy number using oligonucleotide microarrays. Genome Res 14: 287-95.
57. Riegel M. 2014. Human molecular cytogenetics: From cells to nucleotides. Genet Mol Biol 37: 194-209.
58. Cheng J, Vanneste E, Konings P, Voet T, et al. 2011. Single-cell copy number variation detection. Genome Biol 12: R80.
59. Konings P, Vanneste E, Jackmaert S, Ampe M, et al. 2012. Microarray analysis of copy number variation in single cells. Nat Protoc 7: 281-310.
60. Raghavan M, Lillington DM, Skoulakis S, Debernardi S, et al. 2005. Genome-wide single nucleotide polymorphism analysis reveals frequent partial uniparental disomy due to somatic recombination in acute myeloid leukemias. Cancer Res 65: 375-8.
61. Gijsbers ACJ, Ruivenkamp CAL. 2011. Molecular karyotyping: from microscope to SNP arrays. Horm Res Pædiatr 76: 208-13.
62. Lönnstedt IM, Caramia F, Li J, Fumagalli D, et al. 2014. Deciphering clonality in aneuploid tumors using SNP array and sequencing data. Genome Biol 15: 470.
63. Fan HC, Wang J, Potanina A, Quake SR. 2011. Whole-genome molecular haplotyping of single cells. Nat Biotechnol 29: 51-7.
64. Navin N, Kendall J, Troge J, Andrews P, et al. 2011. Tumour evolution inferred by single-cell sequencing. Nature 472: 90-4.
65. Falconer E, Hills M, Naumann U, Poon SSS, et al. 2012. DNA template strand sequencing of single-cells maps genomic rearrangements at high resolution. Nat Methods 9: 1107-12.
66. McConnell MJ, Lindberg MR, Brennand KJ, Piper JC, et al. 2013. Mosaic copy number variation in human neurons. Science 342: 632-7.
67. Cai X, Evrony GD, Lehmann HS, Elhosary PC, et al. 2014. Single-cell, genome-wide sequencing identifies clonal somatic copy-number variation in the human brain. Cell Rep 8: 1280-9.
68. Korbel JO, Campbell PJ. 2013. Criteria for inference of chromothripsis in cancer genomes. Cell 152: 1226-36.
69. Voet T, Kumar P, Van Loo P, Cooke SL, et al. 2013. Single-cell paired-end genome sequencing reveals structural variation per cell cycle. Nucleic Acids Res 41: 6119-38.
70. Macaulay IC, Voet T. 2014. Single cell genomics: Advances and future perspectives. PLoS Genet 10: e1004126.
71. Frumkin D, Wasserstrom A, Itzkovitz S, Harmelin A, et al. 2008. Amplification of multiple genomic loci from single cells isolated by laser micro-dissection of tissues. BMC Biotechnol. 8: 17.
72. Dean FB, Hosono S, Fang L, Wu X, et al. 2002. Comprehensive human genome amplification using multiple displacement amplification. Proc Natl Acad Sci USA 99: 5261-6.
73. Lansdorp PM. 2007. Immortal strands? Give me a break. Cell 129: 1244-7.
74. Hills M, O'Neill K, Falconer E, Brinkman R, et al. 2013. BAIT: organizing genomes and mapping rearrangements in single cells. Genome Med 5: 82.
75. Falconer E, Chavez EA, Henderson A, Poon SSS, et al. 2010. Identification of sister chromatids by DNA template strand sequences. Nature 463: 93-7.
76. Weise A, Heller A, Starke H, Mrasek K, et al. 2003. Multitude multicolor chromosome banding (mMCB) - a comprehensive one-step multicolor FISH banding method. Cytogenet Genome Res 39: 34-9.
77. Vorsanova SG, Yurov YB, Iourov IY. 2010. Human interphase chromosomes: a review of available molecular cytogenetic technologies. Mol Cytogenet 3: 1.