Figure 4: Detecting copy-number alterations from SNP imbalances.
From: Reliable detection of subclonal single-nucleotide variants in tumour cell populations
(a–c) Allele frequencies of known SNPs in matched tumour-normal samples. (a) Tumour 1, (b) tumour 2, (c) tumour 3. Light colours denote the frequency in the normal control, dark colours denote the frequency in the tumour. A deviation from heterozygous SNP frequencies of 0.5 indicates loss of heterozygosity (LOH). (d–f) Copy number profiles and logarithmic probe intensities of 1 M SNP arrays for the samples presented in panel (a–c). (g) Fraction of cells with LOH. The difference of heterozygous SNP frequencies on chromosome 3 (chr3) allows for computing the number of cells carrying only one copy. The resulting fraction of 43% is conserved across the three tumour samples of the same patient. (h) Histology of RCC. CD34-positive, non-cancerous cells (brown) in the primary RCC tissue sample. Nuclei are stained blue. The scale bar denotes 100 μm.
