Automated Screening for Genomic Imbalances in Multiple Myeloma Using Microarray-Based Comparative Genomic Hybridization (mCGH).
Authors: Wendl Christiane , Radlwimmer Bernhard , Wessendorf Swen , Schwaenen Carsten , Döhner Hartmut , Lichter Peter , Liebisch Peter 
Published: April 2020

Abstract
Background: Chromosomal abnormalities are detectable in virtually all patients with multiple myeloma (MM) by the use of molecular cytogenetic techniques (e.g. fluorescence in-situ hybridization, FISH; comparative genomic hybridization, CGH). Genomic rearrangements play a crucial role in the pathogenesis of clonal plasma cell disorders and can deliver important prognostic information. Microarray-based comparative genomic hybridization (mCGH) is an innovative technique that enables a genome-wide, high-resolution tumor cell screening for chromosomal imbalances in a single experiment. The aim of the present study was the detailed characterization of genomic gains and losses in MM - in particular the delineation of critical regions - by the use of mCGH.
Methods: So far, bone marrow specimens from 55 patients with Salmon &Durie stage II or III MM were analyzed. To achieve a plasma cell proportion greater than 50% before hybridization, CD 138-enrichment by immunomagnetic separation was performed whenever necessary. mCGH chips consisting of approximately 6.400 DNA clones, among them ~3.200 clones covering the whole human genome in 1 Mb increments, the remaining forming contigs from specific genomic regions or containing tumor-relevant genes were applied.
Results: 52 out of 55 patients (94.5%) were evaluable by mCGH. Gains and losses of chromosomal material were found in 51 out of 52 patients (98%). In one case, mCGH did not exhibit imbalances but +9q34 and +11q25 was diagnosed by FISH for yet unknown reasons. Genomic losses most frequently involved chromosomes 13 (65%), 1p (39%), 16 (31%), 6 (27%), and 12 (21%), while gains commonly affected chromosomes 1q, 9, 11, 15 (46%), and 19 (35%). High-level amplifications were identified on chromosome 16 in two cases (overall three amplicons involving chromosome bands 16p11-p13, 16q12, and 16q21, respectively) as well as on chromosomes 8 (three amplified segments, one of them containing c-myc at 8q24) and 20q (2 amplifications involving bands 20q13.1 and 20q13.3) in one case each. Data on chromosome 13 deletion was consistent with monosomy 13 in 28 out of 34 cases (82.3%). For the remaining 6 cases with a partial 13q loss, no commonly deleted region could be delineated. In contrast, single critical regions were identified on other chromosomes, e.g. chromosome 14 (+14q23.2-q24.3). A small genomic region defined by only four closely adjacent 11q DNA clones was gained in 23 out of 24 (96%) cases with chromosome 11 extra copies.
Conclusions: mCGH allows the detection of genomic imbalances including high-level amplifications in almost all patients with MM and enables a precise delineation of critical regions in this disease. Evaluation of mCGH raw data is ongoing and confirmative FISH analyses are currently under way. Supported by grants from the Deutsche José Carreras Leukämie-Stiftung (DJCLS-R04/04) and the Wilhelm Sander-Stiftung (No. 2002.098.1) to P.L.