To view the fulltext, please log in
To view the pdf, please log in
- FullText & PDF
- Unlimited re-access via MyKarger (new!)
- Unrestricted printing, no saving restrictions for personal use
- Reduced rates with a PPV account
- Rent for 48h to view
- Buy Cloud Access for unlimited viewing via different devices
- Synchronizing in the ReadCube Cloud
- Printing and saving restriction apply
Rental: USD 8.50
Cloud: USD 20.00
- Automatic perpetual access to all articles of the subscribed year(s)
- Unlimited re-access via Subscriber Login or MyKarger
- Unrestricted printing, no saving restrictions for personal use
Article / Publication Details
Examination of the whole genome for copy number alterations by microarray is now routinely done in many laboratories. The field of cytogenetics has evolved to adapt this technology, and the current phase of transition has resulted in the need for standardization in methodologies and interpretation of data. This review will outline some of the changes addressed in the field over the last several years and briefly discuss some of the trends in data processing, analysis and interpretation.
Article / Publication Details
Copyright / Drug Dosage
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 or, in the case of photocopying, direct payment of a specified fee to the Copyright Clearance Center.
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 goverment 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.
- Albertson DG, Ylstra B, Segraves R, Collins C, Dairkee SH, et al: Quantitative mapping of amplicon structure by array CGH identifies CYP24 as a candidate oncogene. Nat Genet 25:144–146 (2000).
- Alkuraya FS: Homozygosity mapping: one more tool in the clinical geneticist’s toolbox. Genet Med 12:236–239 (2010).
- Aradhya S, Cherry AM: Array-based comparative genomic hybridization: clinical contexts for targeted and whole-genome designs. Genet Med 9:553–559 (2007).
- Aston E, Whitby H, Maxwell T, Glaus N, Cowley B, et al: Comparison of targeted and whole genome analysis of postnatal specimens using a commercially available array based comparative genomic hybridisation (aCGH) microarray platform. J Med Genet 45:268–274 (2008).
- Baldwin EL, Lee JY, Blake DM, Bunke BP, Alexander CR, et al: Enhanced detection of clinically relevant genomic imbalances using a targeted plus whole genome oligonucleotide microarray. Genet Med 10:415–429 (2008).
- Bastian BC, LeBoit PE, Hamm H, Bröcker EB, Pinkel D: Chromosomal gains and losses in primary cutaneous melanomas detected by comparative genomic hybridization. Cancer Res 58:2170–2175 (1998).
- Brothman AR, Dolan MM, Goodman BK, Park JP, Persons DL, et al: College of American Pathologists/American College of Medical Genetics proficienty testing for constitutional cytogenomic microarray analysis. Genet Med (2011), E-pub ahead of print.
- Dougherty MJ, Wilmoth DM, Tooke LS, Shaikh TH, Gai X, et al: Implementation of high resolution single nucleotide polymorphism array analysis as a clinical test for patients with hematologic malignancies. Cancer Genet 204:26–38 (2011).
- Firth HV, Richards SM, Bevan AP, Clayton S, Corpas M, et al: DECIPHER: Database of Chromosomal Imbalance and Phenotype in Humans Using Ensembl Resources. Am J Hum Genet 84:524–533 (2009).
- Friedman JM, Baross A, Delaney AD, Ally A, Arbour L, et al: Oligonucleotide microarray analysis of genomic imbalance in children with mental retardation. Am J Hum Genet 79:500–513 (2006).
- Fujita PA, Rhead B, Zweig AS, Hinrichs AS, Karolchik D, et al: The UCSC Genome Browser database: update 2011. Nucleic Acids Res 39:D876–D882 (2011).
- 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).
- Kearney HM, South ST, Wolff DJ, Lamb A, Hamosh A, et al: American College of Medical Genetics recommendations for the design and performance expectations for clinical genomic copy number microarrays intended for use in the postnatal setting for detection of constitutional abnormalities. Genet Med 13:676–679 (2011a).
- Kearney HM, Thorland EC, Brown KK, Quintero-Rivera F, South ST; A Working Group of the American College of Medical Genetics (ACMG) Laboratory Quality Assurance Committee: American College of Medical Genetics standards and guidelines for interpretation and reporting of postnatal constitutional copy number variants. Genet Med 13:680–685 (2011b).
- Koolen DA, Vissers LE, Pfundt R, de Leeuw N, Knight SJ, et al: A new chromosome 17q21.31 microdeletion syndrome associated with a common inversion polymorphism. Nat Genet 38:999–1001 (2006).
- Lupski JR, Stankiewicz P: Genomic disorders: molecular mechanisms for rearrangements and conveyed phenotypes. PLos Genet 1:e49 (2005).
- Mefford HC, Eichler EE: Duplication hotspots, rare genomic disorders, and common disease. Curr Opin Genet Dev 19:196–204 (2009).
- Miller DT, Adam MP, Aradhya S, Biesecker LG, Brothman AR, et al: Consensus statement: chromosomal microarray is a first-tier clinical diagnostic test for individuals with developmental disabilities or congenital anomalies. Am J Hum Genet 86:749–764 (2010).
- Moreno-De-Luca D; SGENE Consortium, Mulle JG; Simons Simplex Collection Genetics Consortium, Kaminsky EB, et al: Deletion 17q12 is a recurrent copy number variant that confers high risk of autism and schizophrenia. Am J Hum Genet 87:618–630 (2010).
- Nupponen NN, Hyytinen ER, Kallioniemi AH, Visakorpi T: Genetic alterations in prostate cancer cell lines detected by comparative genomic hybridization. Cancer Genet Cytogenet 101:53–57 (1998).
- Papenhausen P, Schwartz S, Risheg H, Keitges E, Gadi I, et al: UPD detection using homozygosity profiling with a SNP genotyping microarray. Am J Med Genet A 155A:757–768 (2011).
- Rauch A, Ruschendorf F, Huang J, Trautmann U, Becker C, et al: Molecular karyotyping using an SNP array for genomewide genotyping. J Med Genet 41:916–922 (2004).
- Sahoo T, Cheung SW, Ward P, Darilek S, Patel A, et al: Prenatal diagnosis of chromosomal abnormalities using array-based comparative genomic hybridization. Genet Med 8:719–727 (2006).
- 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, Saleki R, Rorem E, Sundin K, et al: Targeted genomic microarray analysis for identification of chromosome abnormalities in 1500 consecutive clinical cases. J Pediatr 149:98–102 (2006).
- Shaffer LG, Theisen A, Bejjani BA, Ballif BC, Aylsworth AS, et al: The discovery of microdeletion syndromes in the post-genomic era: review of the methodology and characterization of a new 1q41q42 microdeletion syndrome. Genet Med 9:607–616 (2007).
- Sharp AJ, Hansen S, Selzer RR, Cheng Z, Regan R, et al: Discovery of previously unidentified genomic disorders from the duplication architecture of the human genome. Nat Genet 38:1038–1042 (2006).
- Sharp AJ, Selzer RR, Veltman JA, Gimelli S, Gimelli G, et al: Characterization of a recurrent 15q24 microdeletion syndrome. Hum Mol Genet 16:567–572 (2007).
- Shaw-Smith C, Pittman AM, Willatt L, Martin H, Rickman L, et al: Microdeletion encompassing MAPT at chromosome 17q21.3 is associated with developmental delay and learning disability. Nat Genet 38:1032–1037 (2006).
- Van den Veyver IB, Patel A, Shaw CA, Pursley AN, Kang SH, et al: Clinical use of array comparative genomic hybridization (aCGH) for prenatal diagnosis in 300 cases. Prenat Diagn 29:29–39 (2009).
- Vermeesch JR, Fiegler H, de Leeuw N, Szuhai K, Schoumans J, et al: Guidelines for molecular karyotyping in constitutional genetic diagnosis. Eur J Hum Genet 15:1105–1114 (2007).
- Yatsenko SA, Shaw CA, Ou Z, Pursley AN, Patel A, et al: Microarray-based comparative genomic hybridization using sex-matched reference DNA provides greater sensitivity for detection of sex chromosome imbalances than array-comparative genomic hybridization with sex-mismatched reference DNA. J Mol Diagn 11:226–237 (2009).
- Zhang J, Feuk L, Duggan GE, Khaja R, Scherer SW: Development of bioinformatics resources for display and analysis of copy number and other structural variants in the human genome. Cytogenet Genome Res 115:205–214 (2006).