Chromosomal alterations in 77 MCL cases determined by 500K SNP arrays. Chromosomal alterations in 72 cyclin D1–positive and 5 cyclin D1–negative primary MCL cases determined by 500K SNP arrays. (A) Copy number alterations (including putative copy number variations) according to the CNAG software. Gains are displayed in red on the right side of the ideograms, and losses are shown in green on the left side of the ideograms. (B) Regions of CNN-LOH, also termed UPD; more than 10 Mb determined by the CNAG/AsCNAR and CNAT software tools. Regions of CNN-LOH/UPD are shown in blue, and regions of uniparental trisomy are shown in purple. (Insets) Regions of partial CNN-LOH/UPD in chromosomes 1, 9, and 13 that include small regions of homozygous deletions in 1p32.3/33 (contains the genomic loci of CDKN2C and FAF1), 9p21.3 (CDKN2A locus), and 13q13.3 (containing C13orf36, RFXAP, and SMAD9), indicating that the CNN-LOH/UPD arose after the loss of one copy of the respective genomic locus. The black line indicates total gene dosage; the diploid state is indicated by 2. The red and green lines indicate allele-specific gene dosage levels, with loss of one parental copy and gain of the other in the region of partial CNN-LOH/UPD.