Raw paired allele B fractions. Paired observed allele B fractions, (β
), of tumor TCGA-23-1027 versus its matched normal in six regions of constant PCN for the tumor. Top panels: normal (left), gained (middle), and copy-neutral LOH (right) regions from chromosome 2. Bottom panels: normal (left), deleted (middle), and copy-neutral LOH (right) regions from chromosome 10. SNPs called homozygous (AA and BB) are in gray. Linear models were robustly fitted to the heterozygous SNPs above and below the diagonal (black lines). Black discs mark the center of each cloud.