Published online before print August 7, 2008

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Copyright © 2008 American Society for Investigative Pathology
Journal of Molecular Diagnostics, doi:10.2353/jmoldx.2008.080033

Accepted for publication May 15, 2008.

Article

Whole-Genome Scanning by Array Comparative Genomic Hybridization as a Clinical Tool for Risk Assessment in Chronic Lymphocytic Leukemia

Shelly R. Gunn^*@, Mansoor S. Mohammed, Mercedes E. Gorre, Philip D. Cotter, Jaeweon Kim, David W. Bahler, Sergey N. Preobrazhensky, Russell A. Higgins^*, Aswani R. Bolla^*, Sahar H. Ismail^*, Daphne de Jong, Eric Eldering^¶, Marinus H.J. van Oers^||, Clemens H.M. Mellink^**, Michael J. Keating, Ellen J. Schlette, Lynne V. Abruzzo, and Ryan S. Robetorye^*

From the Department of Pathology,* The University of Texas Health Science Center at San Antonio, San Antonio, Texas; the Departments of Leukemia and Hematopathology, University of Texas M.D. Anderson Cancer Center, Houston, Texas; Combimatrix Molecular Diagnostics Incorporated, Irvine, California; the Department of Pathology and ARUP Institute for Clinical and Experimental Pathology, University of Utah, Salt Lake City, Utah; the Department of Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands; and the Departments of Experimental Immunology,^¶ Hematology,^|| and Clinical Genetics,** Academic Medical Center, Amsterdam, The Netherlands

^@ To whom correspondence should be addressed. E-mail: gunn{at}uthscsa.edu.

	Abstract

Array-based comparative genomic hybridization (array CGH) provides a powerful method for simultaneous genome-wide scanning and prognostic marker assessment in chronic lymphocytic leukemia (CLL). In the current study, commercially available bacterial artificial chromosome and oligonucleotide array CGH platforms were used to identify chromosomal alterations of prognostic significance in 174 CLL cases. Tumor genomes were initially analyzed by bacterial artificial chromosome array CGH followed by confirmation and breakpoint mapping using oligonucleotide arrays. Genomic changes involving loci currently interrogated by fluorescence in situ hybridization (FISH) panels were detected in 155 cases (89%) at expected frequencies: 13q14 loss (47%), trisomy 12 (13%), 11q loss (11%), 6q loss (7.5%), and 17p loss (4.6%). Genomic instability was the second most commonly identified alteration of prognostic significance with three or more alterations involving loci not interrogated by FISH panels identified in 37 CLL cases (21%). A subset of 48 CLL cases analyzed by six-probe FISH panels (288 total hybridizations) was concordant with array CGH results for 275 hybridizations (95.5%); 13 hybridizations (4.5%) were discordant because of clonal populations that comprised less than 30% of the sample. Array CGH is a powerful, cost-effective tool for genome-wide risk assessment in the clinical evaluation of CLL.