The study presents an allele-specific copy number analysis (ASCAT) of breast cancer genomes, aiming to accurately dissect allele-specific copy number while accounting for tumor ploidy and nonaberrant cell admixture. ASCAT calculates "ASCAT profiles" that reveal gains, losses, copy number-neutral events, and loss of heterozygosity (LOH). In an early-stage breast carcinoma series, 45% of cases showed aneuploidy (>2.7n), and the average nonaberrant cell admixture was 49%. ASCAT profiles across the series provide genomic frequency distributions of gains and losses, LOH, and copy number-neutral events. Basal-like breast carcinomas exhibited a significantly higher frequency of LOH compared to other subtypes, with large-scale genomic material loss followed by whole-genome duplication, resulting in near-triploid genomes. ASCAT profiles also reveal differences in aberrant tumor cell fraction, ploidy, gains, losses, LOH, and copy number-neutral events among the five molecular breast cancer subtypes. The study constructs a genome-wide map of allelic skewness, suggesting candidate genes/loci that may drive breast cancer development.The study presents an allele-specific copy number analysis (ASCAT) of breast cancer genomes, aiming to accurately dissect allele-specific copy number while accounting for tumor ploidy and nonaberrant cell admixture. ASCAT calculates "ASCAT profiles" that reveal gains, losses, copy number-neutral events, and loss of heterozygosity (LOH). In an early-stage breast carcinoma series, 45% of cases showed aneuploidy (>2.7n), and the average nonaberrant cell admixture was 49%. ASCAT profiles across the series provide genomic frequency distributions of gains and losses, LOH, and copy number-neutral events. Basal-like breast carcinomas exhibited a significantly higher frequency of LOH compared to other subtypes, with large-scale genomic material loss followed by whole-genome duplication, resulting in near-triploid genomes. ASCAT profiles also reveal differences in aberrant tumor cell fraction, ploidy, gains, losses, LOH, and copy number-neutral events among the five molecular breast cancer subtypes. The study constructs a genome-wide map of allelic skewness, suggesting candidate genes/loci that may drive breast cancer development.