Medical applications of array CGH and the transformation of clinical cytogenetics (original) (raw)
Article navigation
Research Articles| November 24 2006
Signature Genomic Laboratories, LLC, Spokane, WA (USA)
Search for other works by this author on:
Signature Genomic Laboratories, LLC, Spokane, WA (USA)
Search for other works by this author on:
Cytogenet Genome Res (2006) 115 (3-4): 303–309.
Abstract
Microarray-based comparative genomic hybridization (array CGH) merges molecular diagnostics with traditional chromosome analysis and is transforming the field of cytogenetics. Prospective studies of individuals with developmental delay and dysmorphic features have demonstrated that array CGH has the ability to detect any genomic imbalance including deletions, duplications, aneuploidies and amplifications. Detection rates for chromosome abnormalities with array CGH range from 5–17% in individuals with normal results from prior routine cytogenetic testing. In addition, copy number variants (CNVs) were identified in all studies. These CNVs may include large-scale variation and can confound the diagnostic interpretations. Although cytogeneticists will require additional training and laboratories must become appropriately equipped, array CGH holds the promise of being the initial diagnostic tool in the identification of visible and submicroscopic chromosome abnormalities in mental retardation and other developmental disabilities.
References
Ballif BC, Kashork CD, Shaffer LG: The promise and pitfalls of telomere region-specific probes. Am J Hum Genet 67:1356–1359 (2000).
Bejjani BA, Saleki R, Ballif BC, Rorem EA, Sundin K, et al: Use of targeted array-based CGH for the clinical diagnosis of chromosomal imbalance: Is less more? Am J Med Genet A 134:259–267 (2005).
Bossuyt PJ, Van Tienen MN, De Gruyter L, Smets V, Dumon J, Wauters JG: Incidence of low-fluorescence alpha satellite region on chromosome 21 escaping detection of aneuploidy at interphase by FISH. Cytogenet Cell Genet 68:203–206 (1995).
Cheung SW, Shaw CA, Yu W, Li J, Ou Z, et al: Development and validation of a CGH microarray for clinical cytogenetic diagnosis. Genet Med 7:422–432 (2005).
de Vries BB, Pfundt R, Leisink M, Koolen DA, Vissers LE, et al: Diagnostic genome profiling in mental retardation. Am J Hum Genet 77:606–616 (2005).
Flint J, Knight S: The use of telomere probes to investigate submicroscopic rearrangements associated with mental retardation. Curr Opin Genet Dev 13:310–316 (2003).
Greshock J, Naylor TL, Margolin A, Diskin S, Cleaver SH, et al: 1-Mb resolution array-based comparative genomic hybridization using a BAC clone set optimized for cancer gene analysis. Genome Res 14:179–187 (2004).
Hochstenbach R, Meijer J, van de Brug J, Vossebeld-Hoff I, Jansen R, et al: Rapid detection of chromosomal aneuploidies in uncultured amniocytes by multiplex ligation-dependent probe amplification (MLPA). Prenat Diagn 25:1032–1039 (2005).
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).
Ishkanian AS, Malloff CA, Watson SK, DeLeeuw RJ, Chi B, et al: A tiling resolution DNA microarray with complete coverage of the human genome. Nat Genet 36:299–303 (2004).
Jobanputra V, Sebat J, Troge J, Chung W, Anyane-Yeboa K, et al: Application of ROMA (representational oligonucleotide microarray analysis) to patients with cytogenetic rearrangements. Genet Med 7:111–118 (2005).
Kirchhoff M, Gerdes T, Rose H, Maahr J, Ottesen AM, Lundsteen C: Detection of chromosomal gains and losses in comparative genomic hybridization analysis based on standard reference intervals. Cytometry 31:163–173 (1998).
Kirchhoff M, Rose H, Lundsteen C: High resolution comparative genomic hybridisation in clinical cytogenetics. J Med Genet 38:740–744 (2001).
Kirchhoff M, Gerdes T, Brunebjerg S, Bryndorf T: Investigation of patients with mental retardation and dysmorphic features using comparative genomic hybridization and subtelomeric multiplex ligation dependent probe amplification. Am J Med Genet A 139:231–233 (2005).
Knight SJ, Flint J: The use of subtelomeric probes to study mental retardation. Methods Cell Biol 75:799–831 (2004).
Knight SJ, Regan R, Nicod A, Horsley SW, Kearney L, et al: Subtle chromosomal rearrangements in children with unexplained mental retardation. Lancet 354:1676–1681 (1999).
Koolen DA, Nillesen WM, Versteeg MH, Merkx GF, Knoers NV, et al: Screening for subtelomeric rearrangements in 210 patients with unexplained mental retardation using multiplex ligation dependent probe amplification (MLPA). J Med Genet 41:892–899 (2004).
Levy B, Dunn TM, Kaffe S, Kardon N, Hirschhorn K: Clinical applications of comparative genomic hybridization. Genet Med 1:4–12 (1998).
Lichter P, Joos S, Bentz M, Lampel S: Comparative genomic hybridization: uses and limitations. Semin Hematol 37:348–357 (2000).
Ligon AH, Beaudet AL, Shaffer LG: Simultaneous, multilocus FISH analysis for detection of microdeletions in the diagnostic evaluation of developmental delay and mental retardation. Am J Hum Genet 61:51–59 (1997).
Lo AW, Liao GC, Rocchi M, Choo KH: Extreme reduction of chromosome-specific alpha-satellite array is unusually common in human chromosome 21. Genome Res 9:895–908 (1999).
Lucito R, Healy J, Alexander J, Reiner A, Esposito D, et al: Representational oligonucleotide microarray analysis: a high-resolution method to detect genome copy number variation. Genome Res 13:2291–2305 (2003).
Miyake N, Shimokawa O, Harada N, Sosonkina N, Okubo A, et al: BAC array CGH reveals genomic aberrations in idiopathic mental retardation. Am J Med Genet A 140:205–211 (2006).
Pinkel D, Segraves R, Sudar D, Clark S, Poole I, et al: High resolution analysis of DNA copy number variation using comparative genomic hybridization to microarrays. Nat Genet 20:207–211 (1998).
Schouten JP, McElgunn CJ, Waaijer R, Zwijnenburg D, Diepvens F, Pals G: Relative quantification of 40 nucleic acid sequences by multiplex ligation-dependent probe amplification. Nucleic Acids Res 30:e57 (2002).
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).
Shaffer LG, Kashork CD, Bacino CA, Benke PJ: Caution: telomere crossing. Am J Med Genet 87:278–280 (1999).
Shaffer LG, Kashork CD, Saleki R, Rorem E, Sundin K, et al: Targeted genomic microarray analysis for identification of chromosome abnormalities in 1,500 consecutive clinical cases. J Pediatr 49:98–102 (2006).
Shaw-Smith C, Redon R, Rickman L, Rio M, Willatt 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 41:241–248 (2004).
Shevell M, Ashwal S, Donley D, Flint J, Gingold M, et al: Practice parameter: evaluation of the child with global developmental delay: report of the Quality Standards Subcommittee of the American Academy of Neurology and The Practice Committee of the Child Neurology Society. Neurology 60:367–380 (2003).
Snijders AM, Nowak N, Segraves R, Blackwood S, Brown N, et al: Assembly of microarrays for genome-wide measurement of DNA copy number. Nat Genet 29:263–264 (2001).
Stergianou K, Gould CP, Waters JJ, Hulten MA: A DA/DAPI positive human 14p heteromorphism defined by fluorescence in-situ hybridisation using chromosome 15-specific probes D15Z1 (satellite III) and p-TRA-25 (alphoid). Hereditas 119:105–110 (1993).
Verma RS, Luke S: Variations in alphoid DNA sequences escape detection of aneuploidy at interphase by FISH technique. Genomics 14:113–116 (1992).
Verma RS, Batish SD, Gogineni SK, Kleyman SM, Stetka DG: Centromeric alphoid DNA heteromorphisms of chromosome 21 revealed by FISH-technique. Clin Genet 51:91–93 (1997).
Vissers LE, de Vries BB, Osoegawa K, Janssen IM, Feuth T, et al: Array-based comparative genomic hybridization for the genomewide detection of submicroscopic chromosomal abnormalities. Am J Hum Genet 73:1261–1270 (2003).
Vissers LE, van Ravenswaaij CM, Admiraal R, Hurst JA, de Vries BB, et al: Mutations in a new member of the chromodomain gene family cause CHARGE syndrome. Nat Genet 36:955–957 (2004).
Ylstra B, van den Ijssel P, Carvalho B, Brakenhoff RH, Meijer GA: BAC to the future! or oligonucleotides: a perspective for micro array comparative genomic hybridization (array CGH). Nucleic Acids Res 34:445–450 (2006).
© 2006 S. Karger AG, Basel
2006
Copyright / Drug Dosage / Disclaimer
Copyright: All rights reserved. No part of this publication may be translated into other languages, reproduced or utilized in any form or by any means, electronic or mechanical, including photocopying, recording, microcopying, or by any information storage and retrieval system, without permission in writing from the publisher.
Drug Dosage: The authors and the publisher have exerted every effort to ensure that drug selection and dosage set forth in this text are in accord with current recommendations and practice at the time of publication. However, in view of ongoing research, changes in government regulations, and the constant flow of information relating to drug therapy and drug reactions, the reader is urged to check the package insert for each drug for any changes in indications and dosage and for added warnings and precautions. This is particularly important when the recommended agent is a new and/or infrequently employed drug.
Disclaimer: The statements, opinions and data contained in this publication are solely those of the individual authors and contributors and not of the publishers and the editor(s). The appearance of advertisements or/and product references in the publication is not a warranty, endorsement, or approval of the products or services advertised or of their effectiveness, quality or safety. The publisher and the editor(s) disclaim responsibility for any injury to persons or property resulting from any ideas, methods, instructions or products referred to in the content or advertisements.
You do not currently have access to this content.
Sign in
Digital Version
Pay-Per-View Access
$39.00
1 Karger Article Bundle Token
$150
Rental
This article is also available for rental through DeepDyve. 