Copy number alterations and copy number variation in cancer: Close encounters of the bad kind

Cytogenetic and Genome Research

Volumn 123, Issue 1-4, 2009, Pages 176-182

  Speleman, F ^a   Kumps, C ^a   Buysse, K ^a   Poppe, B ^a   Menten, B ^a   De Preter, K ^a  

^a GHENT UNIVERSITY HOSPITAL   (Belgium)

Author keywords

[No Author keywords available]

Indexed keywords

AUTOIMMUNE DISEASE; CANCER GROWTH; CANCER SUSCEPTIBILITY; CARCINOGENESIS; COPY NUMBER VARIATION; GENETIC VARIABILITY; HUMAN IMMUNODEFICIENCY VIRUS INFECTION; PRIORITY JOURNAL; REVIEW;

ANIMALS; EVOLUTION, MOLECULAR; GENE DOSAGE; GENE DUPLICATION; GENETIC PREDISPOSITION TO DISEASE; GENOME; HUMANS; NEOPLASMS;

EID: 62549129879     PISSN: 14248581     EISSN: None     Source Type: Journal    
DOI: 10.1159/000184706     Document Type: Review

References (46)

1. Albertson DG: Gene amplification in cancer. Trends Genet 22:447-455 (2006).
2. Barbouti A, Stankiewicz P, Nusbaum C, Cuomo C, Cook A, et al: The breakpoint region of the most common isochromosome, i(17q), in human neoplasia is characterized by a complex genomic architecture with large, palindromic, low-copy repeats. Am J Hum Genet 74:1-10 (2004).
3. Basecke J, Whelan JT, Griesinger F, Bertrand FE: The MLL partial tandem duplication in acute myeloid leukaemia. Br J Haematol 135:438-449 (2006).
4. Bauters M, Van Esch H, Friez MJ, Boespflug-Tanguy O, Zenker M, et al: Nonrecurrent MECP2 duplications mediated by genomic architecture-driven DNA breaks and break-induced replication repair. Genome Res 18:847-858 (2008).
5. Bignell GR, Santarius T, Pole JC, Butler AP, Perry J, et al: Architectures of somatic genomic rearrangement in human cancer amplicons at sequence-level resolution. Genome Res 17:1296-1303 (2007).
6. Braude I, Vukovic B, Prasad M, Marrano P, Turley S, et al: Large scale copy number variation (CNV) at 14q12 is associated with the presence of genomic abnormalities in neoplasia. BMC Genomics 7:138 (2006).
7. Buysse K, Crepel A, Menten B, Pattyn F, Antonacci F, et al: Mapping of 5q35 chromosomal rearrangements within a genomically unstable region. J Med Genet 45:672-678 (2008).
8. Campbell PJ, Stephens PJ, Pleasance ED, O'Meara S, Li H, et al: Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencing. Nat Genet 40:722-729 (2008).
9. Camps J, Grade M, Nguyen QT, Hormann P, Becker S, et al: Chromosomal breakpoints in primary colon cancer cluster at sites of structural variants in the genome. Cancer Res 68:1284-1295 (2008).
10. Cardone MF, Jiang Z, D'Addabbo P, Archidiacono N, Rocchi M, et al: Hominoid chromosomal rearrangements on 17q map to complex regions of segmental duplication. Genome Biol 9:R28 (2008).
11. Chanalaris A, Brazma D, Rai L, Chanalaris A, Howard J, et al: Genome profile of Ph-positive ALL in adult patients. 13th Congress of the European Hematology Association, Copenhagen, Denmark (2008).
12. Chin L, Gray JW: Translating insights from the cancer genome into clinical practice. Nature 452:553-563 (2008).
13. Collins I, Workman P: New approaches to molecular cancer therapeutics. Nat Chem Biol 2:689-700 (2006).
14. Darai-Ramqvist E, Sandlund A, Muller S, Klein G, Imreh S, Kost-Alimova M: Segmental duplications and evolutionary plasticity at tumor chromosome break-prone regions. Genome Res 18:370-379 (2008).
15. De Raedt T, Stephens M, Heyns I, Brems H, Thijs D, et al: Conservation of hotspots for recombination in low-copy repeats associated with the NF1 microdeletion. Nat Genet 38:1419-1423 (2006).
16. Diskin SJ: A genome-wide association study (GWAS) of copy number variants (CNVs) identifies neuroblastoma predisposition loci. Advances in Neuroblastoma Research meeting, Tokyo, Japan (2008).
17. Feuk L, Carson AR, Scherer SW: Structural variation in the human genome. Nat Rev Genet 7:85-97 (2006).
18. Gibcus JH, Kok K, Menkema L, Hermsen MA, Mastik M, et al: High-resolution mapping identifies a commonly amplified 11q13.3 region containing multiple genes flanked by segmental duplications. Hum Genet 121:187-201 (2007).
19. Graveley BR: Molecular biology: power sequencing. Nature 453:1197-1198 (2008).
20. Heim S, Mitelman F: Molecular screening for new fusion genes in cancer. Nat Genet 40:685-686 (2008).
21. Iafrate AJ, Feuk L, Rivera MN, Listewnik ML, Donahoe PK, et al: Detection of large-scale variation in the human genome. Nat Genet 36:949-951 (2004).
22. Imreh S, Kholodnyuk I, Allikmetts R, Stanbridge EJ, Zabarovsky ER, Klein G: Nonrandom loss of human chromosome 3 fragments from mouse-human microcell hybrids following progressive growth in SCID mice. Genes Chromosomes Cancer 11:237-245 (1994).
23. Kallioniemi A: CGH microarrays and cancer. Curr Opin Biotechnol 19:36-40 (2008).
24. Kidd JM, Cooper GM, Donahue WF, Hayden HS, Sampas N, et al: Mapping and sequencing of structural variation from eight human genomes. Nature 453:56-64 (2008).
25. Lahortiga I, De Keersmaecker K, Van Vlierberghe P, Graux C, Cauwelier B, et al: Duplication of the MYB oncogene in T cell acute lymphoblastic leukemia. Nat Genet 39:593-595 (2007).
26. Laureys G, Versteeg R, Speleman F, van der Drift P, Francke U, et al: Characterisation of the chromosome breakpoints in a patient with a constitutional translocation t(1; 17)(p36.31-p36.13; q11.2-q12) and neuroblastoma. Eur J Cancer 31A:523-526 (1995).
27. Lindsay SJ, Khajavi M, Lupski JR, Hurles ME: A chromosomal rearrangement hotspot can be identified from population genetic variation and is coincident with a hotspot for allelic recombination. Am J Hum Genet 79:890-902 (2006).
28. Mardis ER: The impact of next-generation sequencing technology on genetics. Trends Genet 24:133-141 (2008).
29. Mendrzyk F, Korshunov A, Toedt G, Schwarz F, Korn B, et al: Isochromosome breakpoints on 17p in medulloblastoma are flanked by different classes of DNA sequence repeats. Genes Chromosomes Cancer 45:401-410 (2006).
30. Michels E, De Preter K, Van Roy N, Speleman F: Detection of DNA copy number alterations in cancer by array comparative genomic hybridization. Genet Med 9:574-584 (2007).
31. Mitelman F, Johansson B, Mertens F: The impact of translocations and gene fusions on cancer causation. Nat Rev Cancer 7:233-245 (2007).
32. Mullighan CG, Goorha S, Radtke I, Miller CB, Coustan-Smith E, et al: Genome-wide analysis of genetic alterations in acute lymphoblastic leukaemia. Nature 446:758-764 (2007).
33. Pinkel D, Albertson DG: Array comparative genomic hybridization and its applications in cancer. Nat Genet 37 Suppl:S11-S17 (2005).
34. Redon R, Ishikawa S, Fitch KR, Feuk L, Perry GH, et al: Global variation in copy number in the human genome. Nature 444:444-454 (2006).
35. Saglio G, Storlazzi CT, Giugliano E, Surace C, Anelli L, et al: A 76-kb duplicon maps close to the BCR gene on chromosome 22 and the ABL gene on chromosome 9: possible involvement in the genesis of the Philadelphia chromosome translocation. Proc Natl Acad Sci USA 99:9882-9887 (2002).
36. Samonte RV, Eichler EE: Segmental duplications and the evolution of the primate genome. Nat Rev Genet 3:65-72 (2002).
37. Schmidt L, Duh FM, Chen F, Kishida T, Glenn G, et al: Germline and somatic mutations in the tyrosine kinase domain of the MET proto-oncogene in papillary renal carcinomas. Nat Genet 16:68-73 (1997).
38. Sebat J, Lakshmi B, Troge J, Alexander J, Young J, et al: Large-scale copy number polymorphism in the human genome. Science 305:525-528 (2004).
39. Selzer RR, Richmond TA, Pofahl NJ, Green RD, Eis PS, et al: Analysis of chromosome breakpoints in neuroblastoma at sub-kilobase resolution using fine-tiling oligonucleotide array CGH. Genes Chromosomes Cancer 44:305-319 (2005).
40. Shaw CJ, Lupski JR: Implications of human genome architecture for rearrangement-based disorders: the genomic basis of disease. Hum Mol Genet 13 Spec No 1:R57-R64 (2004).
41. Speicher MR, Carter NP: The new cytogenetics: blurring the boundaries with molecular biology. Nat Rev Genet 6:782-792 (2005).
42. Stranger BE, Forrest MS, Dunning M, Ingle CE, Beazley C, et al: Relative impact of nucleotide and copy number variation on gene expression phenotypes. Science 315:848-853 (2007).
43. Vandepoele K, Van Roy N, Staes K, Speleman F, van Roy F: A novel gene family NBPF: intricate structure generated by gene duplications during primate evolution. Mol Biol Evol 22:2265-2274 (2005).
44. Vandepoele K, Andries V, Van Roy N, Staes K, Vandesompele J, et al: A constitutional translocation t(1; 17)(p36.2;q11.2) in a neuroblastoma patient disrupts the human NBPF1 and ACCN1 genes. PLoS ONE 3:e2207 (2008).
45. Weinberg RA: The Biology of Cancer (Garland Science, Taylor & Francis Group, LLC, Abingdon 2008).
46. Zhang L, Huang J, Yang N, Greshock J, Megraw MS, et al: microRNAs exhibit high frequency genomic alterations in human cancer. Proc Natl Acad Sci USA 103:9136-9141 (2006).