Abstract
Rapid, high-resolution analysis of genomic rearrangements has become possible using array-comparative genomic hybridization (aCGH), a combination of CGH with DNA microarray technology. Using aCGH, genome copy number changes and rearrangement breakpoints can now be mapped and analyzed at resolutions down to a few kilobases or even less in a single hybridization. This technology is enabling us to identify previously hidden rearrangements in patients with suspected genomic disorders for which no karyotype aberrations could be identified using conventional cytogenetic analysis. Furthermore, the development of array painting has revealed a surprising level of rearrangement complexity in patients with apparently balanced translocations.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
Kallioniemi A, Kallioniemi OP, Sudar D, et al. Comparative genomic hybridization for molecular cytogenetic analysis of solid tumors. Science 1992;258:818–821.
Forozan F, Karhu R, Kononen J, Kallioniemi A, Kallioniemi OP. Genome screening by comparative genomic hybridization. Trends Genet 1997;13:405–409.
Lichter P, Fischer K, Joos S, et al. Efficacy of current molecular cytogenetic protocols for the diagnosis of chromosome aberrations in tumor specimens. Cytokines Mol Ther 1996;2:163–169.
Ness GO, Lybaek H, Houge G. Usefulness of high-resolution comparative genomic hybridization (CGH) for detecting and characterizing constitutional chromosome abnormalities. Am J Med Genet 2002;113:125–136.
Kirchhoff M, Rose H, Lundsteen C. High resolution comparative genomic hybridisation in clinical cytogenetics. J Med Genet 2001;38:740–744.
Solinas-Toldo S, Lampel S, Stilgenbauer S, et al. Matrix-based comparative genomic hybridization: biochips to screen for genomic imbalances. Genes Chromosomes Cancer 1997;20:399–407.
Pinkel D, Segraves R, Sudar D, et al. High resolution analysis of DNA copy number variation using comparative genomic hybridization to microarrays. Nat Genet 1998;20:207–211.
Snijders AM, Nowak N, Segraves R, et al. Assembly of microarrays for genome-wide measurement of DNA copy number. Nat Genet 2001;29:263–264.
Buckley PG, Mantripragada KK, Benetkiewicz M, et al. A full-coverage, high-resolution human chromosome 22 genomic microarray for clinical and research applications. Hum Mol Genet 2002;11:3221–3229.
Hodgson G, Hager JH, Volik S, et al. Genome scanning with array CGH delineates regional alterations in mouse islet carcinomas. Nat Genet 2001;29:459–464.
Telenius H, Carter NP, Bebb CE, Nordenskjold M, Ponder BA, Tunnacliffe A. Degenerate oligonucleotideprimed PCR: general amplification of target DNA by a single degenerate primer. Genomics 1992;13:718–725.
Telenius H, Pelmear AH, Tunnacliffe A, et al. Cytogenetic analysis by chromosome painting using DOP-PCR amplified flow-sorted chromosomes. Genes Chromosomes Cancer 1992;4:257–263.
Foreman PK, Davis RW. Real-time PCR-based method for assaying the purity of bacterial artificial chromosome preparations. Biotechniques 2000;29:410–412.
Fiegler H, Carr P, Douglas EJ, et al. DNA microarrays for comparative genomic hybridization based on DOPPCR amplification of BAC and PAC clones. Genes Chromosomes Cancer 2003;36:361–374.
Shaw-Smith C, Redon R, Rickman L, et al. Microarray based comparative genomic hybridisation (array-CGH) detects submicroscopic chromosomal deletions and duplications in patients with learning disability/mental retardation and dysmorphic features. J Med Genet 2004;41:241–248.
Sebat J, Lakshmi B, Troge J, et al. Large-scale copy number polymorphism in the human genome. Science 2004;305:525–528.
Iafrate AJ, Feuk L, Rivera MN, et al. Detection of large-scale variation in the human genome. Nat Genet 2004;36:949–951.
Vissers LE, de Vries BB, Osoegawa K, et al. Array-based comparative genomic hybridization for the genomewide detection of submicroscopic chromosomal abnormalities. Am J Hum Genet 2003;73:1261–1270.
Tyson C, McGillivray B, Chijiwa C, Rajcan-Separovic E. Elucidation of a cryptic interstitial 7q31.3 deletion in a patient with a language disorder and mild mental retardation by array-CGH. Am J Med Genet 2004;129A:254–260.
Fiegler H, Gribble SM, Burford DC, et al. Array painting: a method for the rapid analysis of aberrant chromosomes using DNA microarrays. J Med Genet 2003;40:664–670.
Gribble SM, Prigmore E, Burford DC, et al. The complex nature of constitutional de novo apparently balanced translocations in patients presenting with abnormal phenotypes. J Med Genet 2005;42:8–16.
Snijders AM, Nowee ME, Fridlyand J, et al. Genome-wide-array-based comparative genomic hybridization reveals genetic homogeneity and frequent copy number increases encompassing CCNE1 in fallopian tube carcinoma. Oncogene 2003;22:4281–4286.
Greshock J, Naylor TL, Margolin A, et al. 1-Mb resolution array-based comparative genomic hybridization using a BAC clone set optimized for cancer gene analysis. Genome Res 2004;14:179–187.
Woodfine K, Fiegler H, Beare DM, et al. Replication timing of the human genome. Hum Mol Genet 2004;13:575.
Wang NJ, Liu D, Parokonny AS, Schanen NC. High-resolution molecular characterization of 15q11-q13 rearrangements by array comparative genomic hybridization (array CGH) with detection of gene dosage. Am J Hum Genet 2004;75:267–281.
Zafarana G, Grygalewicz B, Gillis AJ, et al. 12p-amplicon structure analysis in testicular germ cell tumors of adolescents and adults by array CGH. Oncogene 2003;22:7695–7701.
Yu W, Ballif BC, Kashork CD, et al. Development of a comparative genomic hybridization microarray and demonstration of its utility with 25 well-characterized 1p36 deletions. Hum Mol Genet 2003;12:2145–2152.
Shaw CJ, Shaw CA, Yu W, et al. Comparative genomic hybridisation using a proximal 17p BAC/PAC array detects rearrangements responsible for four genomic disorders. J Med Genet 2004;41:113–119.
Redon R, Rio M, Gregory SG, et al. Tiling path resolution mapping of constitutional 1p36 deletions by array-CGH: contiguous gene deletion or’ deletion with positional effect’ syndrome? J Med Genet 2005;42:166–171.
Ishkanian AS, Malloff CA, Watson SK, et al. A tiling resolution DNA microarray with complete coverage of the human genome. Nat Genet 2004;36:299–303.
de Leeuw RJ, Davies JJ, Rosenwald A, et al. Comprehensive whole genome array CGH profiling of mantle cell lymphoma model genomes. Hum Mol Genet 2004;13:1827–1837.
Albertson DG, Ylstra B, Segraves R, et al. Quantitative mapping of amplicon structure by array CGH identifies CYP24 as a candidate oncogene. Nat Genet 2000;25:144–146.
Bignell GR, Huang J, Greshock J, et al. High-resolution analysis of DNA copy number using oligonucleotide microarrays. Genome Res 2004;14:287–295.
Carvalho B, Ouwerkerk E, Meijer GA, Ylstra B. High resolution microarray comparative genomic hybridisation analysis using spotted oligonucleotides. J Clin Pathol 2004;57:644–646.
Lucito R, Healy J, Alexander J, et al. Representational oligonucleotide microarray analysis: a high-resolution method to detect genome copy number variation. Genome Res 2003;13:2291–2305.
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2006 Humana Press Inc., Totowa, NJ
About this chapter
Cite this chapter
Carter, N.P., Fiegler, H., Gribble, S., Redon, R. (2006). Array-CGH for the Analysis of Constitutional Genomic Rearrangements. In: Lupski, J.R., Stankiewicz, P. (eds) Genomic Disorders. Humana Press. https://doi.org/10.1007/978-1-59745-039-3_27
Download citation
DOI: https://doi.org/10.1007/978-1-59745-039-3_27
Publisher Name: Humana Press
Print ISBN: 978-1-58829-559-0
Online ISBN: 978-1-59745-039-3
eBook Packages: MedicineMedicine (R0)