Chromosome analysis suite chas software

Chromosomal abnormalities present in tumor plasma cells were detected either by fluorescence in situ (FISH) for t(4;14)(p16;q32) and del(17p) using specific provided by Abbott Molecular (Paris, France) and Cytocell (Paris, France) according to the manufacturer’s instructions. The del(17p) status was retained only if present in at least 55% of the plasma cells or by single nucleotide polymorphism (SNP) array for 1q gain, del(1p32) targeting CDKN2C and hyperdiploidy previously defined as 47 chromosomes or more [25 (link)]. Hybridization-based genomic profiling arrays were performed using Genome-Wide Human SNP Array 6.0 or the CytoScan HD array, according to the manufacturer’s instructions (Affymetrix, Santa Clara, CA, USA) now part of Thermo Fisher Scientific (Thermo Fisher Scientific, Inc.). Following the procedures of sample preparation, hybridization, and scanning, the CEL file of Genome-Wide Human SNP Array 6.0 was analyzed as previously described [5 (link)] and the CEL file of CytoScan HD array was analyzed using the Chromosome Analysis Suite (ChAS) software (Thermo Fisher Scientific, Inc). Chromosomal changes of each sample were visualized by a diagram of all CNVs, the karyoview, and by visual inspection. Ploidy of tumor plasma cells for each patient was obtained using allele-specific copy number analysis of tumors algorithm (ASCAT 2.2) with default parameters [26 (link)].

Whole-genome level CNA analysis was performed with Cytoscan 750 K array (Thermo Fisher Scientific) according to the protocol provided by the manufacturer. Data were analysed using Chromosome Analysis Suite (ChAS) software (Thermo Fisher Scientific). The reference database included the Database of Genomic Variants (GRCh38/hg38).