Copy number profiles of chromosome 2 and 13 in 6 CLL patients. The x-axis shows physical position along the chromosome. Red and blue colors indicate copy number loss and gain as well as the −log₁₀ copy number–associated P value in the top and middle panels, respectively. The y-axis (bottom panel) indicates −log₁₀P value that homozygous stretches are due to chance. (A) Copy number and LOH profiles of 4 CLL patients with gains of chromosome 2p. Black rectangle indicates smallest region of overlap among the 4 aberrations. This gain of 3.5 Mb in patient no. 3 spans the REL and BCL11A oncogenes. (B) Copy number and LOH profile of chromosome 13 in 2 patients. Top panel shows biallelic deletion of the 13q14 region and LOH for almost the whole chromosome, indicative of a somatic recombination event. Due to the presence of normal cells, the LOH profile is not uniform because heterozygous SNP calls are still present and prevent more significant values. Bottom panel shows a profile of chromosome 13 with normal copy number but 3 large LOH regions totaling up to 40 Mb. The more proximal LOH spans the MIRN genes from the 13q14 region. These LOH regions are also present in the germline from this patient.