FIG 1.

Copy number neutral loss of heterozygosity (LOH) is seen on chromosome 18 in tumors isolated from Apc^min/+ mice. (A) LOH score for each autosomal chromosome. For each chromosome, all positions along the chromosome were averaged to create an LOH score for that chromosome. Only chromosomes with large regions of LOH will show a significantly decreased fraction of reads aligning to the reference allele. (B) Location of LOH along chromosome 18. The position on the x axis represents the median chromosomal position taken from the following four intervals along chromosome 18: 3.4 × 10⁷ to 3.5 × 10⁷, 3.6 × 10⁷ to 3.7 × 10⁷, 3.7 × 10⁷ to 3.8 × 10⁷, and 3.8 × 10⁷ to 3.9 × 10⁷. The Apc gene is located in the first interval. Error bars represent standard error of the mean. At a position that has lost heterozygosity, the fraction of reads aligning to the reference allele is expected to be considerably lower than 0.5. (C) Copy number variations on chromosome 18 in Apc^min/+ sham and Apc^min/+ ETBF tumor samples as determined by CNVkit. Each gray dot represents an individual data point, and the orange lines/dot represent the average copy number variation over a given region of chromosome 18. A log₂ copy ratio of 0 represents no difference in copy number at that location between the tumor sample and a normal sample from the same mouse.