We begin by describing the inference framework used in the ABSOLUTE method. Suppose a cancer-tissue sample consists of a mixture of a proportion α of cancer cells (assumed to be monogenomic – that is, with homogenous SCNAs in the cancer cells) and a proportion (1-α) of contaminating normal (diploid) cells. For each locus x in the genome, let q(x) denote the integer copy-number of the locus in the cancer cells. Let τ denote the mean ploidy of the cancer-cell fraction, defined as the average value of q(x) across the genome. In the mixed cancer sample, the average absolute copy number of locus x is αq(x) + 2(1 - α) and the average ploidy is D = ατ+ 2(1 - α), measured in units of haploid genomes.
