Cytogenomics software version 4

To detect copy number alterations, array comparative genomic hybridization (aCGH) was performed on amplified DNA from CD138 + cells, utilizing the oligonucleotidebased 8 × 60K array according to the manufacturer's protocol (Agilent Technologies, Santa Clara, CA). Amplified DNA samples from healthy male and female subjects were used as reference. Samples were hybridized on the array chip for 18 to 24 hours, then washed and scanned into image files using an Agilent microarray scanner (model PN G2565BA). Microarray analysis was performed using Cytogenomics software version 4.0 (Agilent). For any given region, gains and losses were reported from a minimum of 100 consecutive probes or at least 0.5 Mb in size, with an absolute mean log 2 ratio of >0.2 and <-0.3, respectively. The reproducibility of microarray results was assessed by analysis of DNA obtained after the amplification of a second aliquot from the same sample. Microarray experiments were also performed on the same set of DNA samples to determine inter-and intrarun variability. FISH studies for randomly selected loci were performed to corroborate microarray findings. In all instances, FISH results were concordant with the findings of microarray. Thus, there was no evidence of false-positive results due to whole-genome amplification.