Fig. 3
Assay quality. (a) DNA Quality Control. Points: PDX tumor sample that did (green) or didn’t (red) meet quality control standards. Sample quality was empirically based on: the total number of mapped reads (set to be >106, vertical dashed line); and the percentage reads mapped to expected amplicons (set to be >85%, horizontal dashed line). (b) RNA Quality Control. Points/colors as in a. Sample quality was empirically based on: the % of ~22 K genes that had reads mapped to them (set to be >45%, vertical dashed line); and the average length of reads (set to be >100, horizontal dashed line). (c) DNA Mouse contribution. DNA sequencing was run on PDX and pure mouse samples; mutation calls were made against the reference human genome. Plot depicts variant Allele Frequency (y-axis) in our PDX samples as a function of PDX sample (x-axis) for loci (curves) that are called as mutated in mouse (red) or not (blue). The PDX samples are sorted (x-axis) based on the variant allele frequency across the loci that are mutated in mouse (i.e. the red curves go up from left to right). Color bar: PDX model. Note: Loci that are called mutant in mouse and human are candidate false positives, i.e. potentially unmutated in human and driven purely by mouse contribution. The fraction of mutant reads would be expected to co-vary across loci depending on the degree of mouse contamination. (d) Effect of mouse on RNA. Scatter plots comparing expression of “non-low” expressing genes for sample #3 either: left) from a pair of technical replicates in the main experiment, or right) with (y-axis) and without (x-axis) a spike-in of 10% mouse. Genes are colored by whether they do (red) or do not (green) lie above the red dashed line (2*(x - y)/(x + y) > 0.5). (e) Sample IF images of marker sets in healthy mouse colon. Arrows indicate expected staining patterns, e.g. crypt localization for Ki67 showing proliferating cells (MS2), localization of β-catenin and E-cadherin at cell-cell junctions (MS1 and MS3), and extracellular staining by Vimentin (all MSs).
