The 50k SNP array platform can detect single copy chromosomal differences in the CLL genome with high sensitivity and specificity. DNA from FACS-sorted CD19⁺ cells and buccal cells was extracted and prepared for hybridization to the 50kXbaI SNP chips as per manufacturer's recommendation. Copy number estimates for each SNP position were calculated using dChipSNP and displayed for all SNP positions, for all patients, for the indicated chromosomes. Copy losses are displayed with blue colors; copy gains, with red colors. The physical position of SNPs is not linear along the displayed portions of the chromosome. (A) Chromosome X. Color-coded copy number estimates are grouped by the known sex of the patients. Red asterisks indicate females with LOH at chromosome X indicating loss. The estimated copy numbers for all SNP positions for CLL no. 105 are displayed along the entire chromosome to the right of the X chromosome display, with the red line indicating the 2N state. (B) Chromosome 12. All patients with FISH results positive for trisomy 12 are grouped on the left of the image. The estimated copy numbers for all SNP positions for CLL no. 143 is shown along the entire chromosome to the right of the chromosome 12 display, with the red line indicating the 2N state. Sporadic subchromosomal copy losses are encircled with red ovals. The approximate position of the clinically used trisomy 12 FISH probe is indicated.