Homozygous deletions in MCL cell lines detected by SNP array and qPCR. (A) Profiles of chromosomes 1 and 2 detected by the SNP array in 3 MCL cell lines, represented from pter (left) to qter (right). GSA P values represent copy number alterations. The lowest values (vertical red lines) pointed by arrows highlight regions with homozygous deletions and candidate genes. UPN1 showed a novel homozygous deletion including FAF1 gene at 1p32.3, whereas JEKO1 and MINO showed 2 concomitant homozygous deletions at 2q12.1 and 2q37, targeting BCL2L11 and SP100 genes, respectively. In addition, JEKO1 showed 2p gain and MINO gain of whole chromosome 2. (B) Representation of FAF1 and SP100 gene qPCR validation. For each gene, the copy number alteration (upper panel SNP array and lower panel qPCR) and expression values (top panel expression array and bottom panel qRT-PCR) are shown. The color codes for the DNA analysis represent the copy number changes and show a high concordance between the results of the respective techniques. Similarly, the relative mRNA expression levels are represented in a color scale (from green to red, indicating low to high expression, respectively) and also show a high concordance of the results. The genes included in the homozygous deleted regions (FAF1 in UPN1 and SP100 in JEKO1 and MINO) had undetectable mRNA levels supporting their inactivation in these MCL cell lines.