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Estimation of allele-specific copy number (ASCN), which quantifies the number of copies of each allele at each variant loci rather than the total number of chromosome copies, is an important step in the characterization of tumor genomes and the inference of their clonal history. Sequencing produces reads containing both alleles at heterozygous variant loci, and thus, like genotyping arrays, allows the disambiguation of ASCNs. Compared to genotyping arrays, next-generation sequencing can provide finer resolution in estimating ASCNs because each person has his/her own unique heterozygous variant loci that are not included in regular genotyping arrays.
(Chen et al., 2015) Allele-specific copy number profiling by next-generation DNA sequencing. Nucleic Acids Research.