GENES, CHROMOSOMES & CANCER 48:603–614 (2009) A SNP Microarray and FISH-Based Procedure to Detect Allelic Imbalances in Multiple Myeloma: An Integrated Genomics Approach Reveals a Wide Gene Dosage Effect Luca Agnelli, 1 Laura Mosca, 1 Sonia Fabris, 1 Marta Lionetti, 1 Adrian Andronache, 1 Ivo Kwee, 2 Katia Todoerti, 1 Donata Verdelli, 1 Cristina Battaglia, 3 Francesco Bertoni, 2 Giorgio Lambertenghi Deliliers, 1 and Antonino Neri 1 * 1 Department of Medical Sciences,University of Milano and Hematology 1-CTMO, Fondazione IRCCS Ospedale Maggiore Policlinico Mangiagalli Regina Elena, Milano, Italy 2 Laboratory of Experimental Oncology,Oncology Institute of Southern Switzerland,Bellinzona, Switzerland 3 Department of Biomedical Sciences and Technologies,CISI,University of Milan, Italy Multiple myeloma (MM) is characterized by marked genomic heterogeneity. Beyond structural rearrangements, a relevant role in its biology is represented by allelic imbalances leading to significant variations in ploidy status. To elucidate better the genomic complexity of MM, we analyzed a panel of 45 patients using combined FISH and microarray approaches. We firstly generated genome-wide profiles of 41 MMs and four plasma cell leukemias, using a self-developed procedure to infer exact local copy numbers (CNs) for each sample. Our analysis allowed the identification of a significant fraction of patients showing near-tetraploidy. Furthermore, a conventional hierarchical clustering analysis showed that near-tetraploidy, 1q gain, hyperdiploidy, and recursive deletions at 1p and chromosomes 13, 14, and 22 were the main aberrations driving samples grouping. Moreover, mapping information was integrated with gene expression profiles of the tumor samples. A multiclass analysis of transcriptional profiles characterizing the different clusters showed marked gene-dosage effects, particularly con- cerning 1q transcripts; this finding was also confirmed by a nonparametric analysis between normalized gene expression levels and local CN variations (1027 highly-significant correlated genes). Finally, we identified several loci in which gene expression correlated with the occurrence of loss of heterozygosity. Our results provide insights into the composite net- work linking genome structure and transcriptional features in MM. V V C 2009 Wiley-Liss, Inc. INTRODUCTION Multiple myeloma (MM) is a malignant plasma cell disorder characterized by a profound genomic heterogeneity that involves both numerical and structural chromosomal rearrangements (Fonseca et al., 2004). Nearly half of MM tumors are hyperdiploid (47–74 chromosomes), showing multiple trisomies of nonrandom odd-numbered chromosomes and a low prevalence of immuno- globulin heavy chain (IGH) translocations and chromosome 13 deletion (Fonseca et al., 2004). The remaining tumors are nonhyperdiploid, fre- quently showing chromosome 13 deletion, 1q gain, and chromosomal translocations involving the IGH locus on chromosome 14q32 (Bergsagel and Kuehl, 2005). Among the nonhyperdiplod cases, different groups can be identified based on chromosome content: hypodiploid (<44 chromo- somes), pseudodiploid (45–46 chromosomes), near-tetraploid (more than 75 chromosomes) (Fonseca et al., 2004). We and others have exten- sively demonstrated the occurrence of specific transcriptional patterns associated with the major genetic lesions in MM (Shaughnessy et al., 2003, 2007; Hideshima et al., 2004; Agnelli et al., 2005; Bergsagel and Kuehl, 2005; Zhan et al., 2006; Agnelli et al., 2007a,b; Chng et al., 2007; Fabris et al., 2007a). Many comprehensive cytogenetic analyses (conventional cytogenetics, CGH) have been per- formed in MM, and recurrent copy number (CN) changes have been described, which may contrib- ute to MM heterogeneity (Cigudosa et al., 1998; Gutierrez et al., 2004; Liebisch and Dohner, Additional Supporting Information may be found in the online version of this article. Supported by: Associazione Italiana Ricerca sul Cancro to A.N.; Ministero Italiano della Salute; Associazione Italiana contro le Leucemie (AIL) di Milano; Cantone Ticino ‘‘Ticino in rete’’ to F.B. and I.K.; Fondazione per la Ricerca e la Cura dei Linfomi (Lugano, Switzerland) to F.B. and I.K.; fellowships from Fonda- zione Italiana Ricerca sul Cancro to L.A. and K.T. *Correspondence to: Antonino Neri, Department of Medical Sciences, University of Milan, F. Sforza 35, 20122 Milano, Italy. E-mail: antonino.neri@unimi.it Received 19 January 2009; Accepted 31 March 2009 DOI 10.1002/gcc.20668 Published online 24 April 2009 in Wiley InterScience (www.interscience.wiley.com). V V C 2009 Wiley-Liss, Inc.