Figure 5.

Genomic profile of tumor components. The uppermost plot for each sample represents the estimated copy number as a log 2 ratio averaged over 30 SNPs; middle bar represents a color-coded Hidden Markov Model (HMM) for copy number (yellow = copy number 2, pink = copy number 3, aqua = copy number 1), and bottom bar is a color-coded HMM for LOH (yellow = no LOH, blue = LOH). Genomic analysis revealed loss of chromosome 3p and gains in chromosomes 5 and 7 in all ccRCC components, a gain of 2p and loss of 10q in the oncocytic component, and a profile consistent with polyploidy (likely trisomic) with additional gains and losses in the high-grade component. The tubulocystic component showed a profile distinct from that of ccRCC. Germline uniparental disomy (UPD) of chromosomes 2 and 6 [UPD2 (q21.3-q22.1), UPD6 (q23.2-q23.3)] (asterisks) was found in all (tumor and normal) specimens from the patient.