Next-generation sequencing of human tumor xenografts is significantly improved by prior depletion of mouse cell

Human tumor xenografts represent the gold standard method for many research areas, including drug discovery, cancer stem cell biology, and metastasis prediction. When compared to in vitro cell culture models, human tumor xenografts show a higher validity for most assays1. During the growth phase in vivo, xenografted tissue is vascularized and infiltrated by cells of murine origin. The level of infiltration is highly dependent on multiple factors like tumor subtype, growth rate, and region of transplantation. However, even when these factors are kept constant, the amount and composition of infiltrating mouse cells is highly variable. Due to this, molecular downstream analyses such as microarray-based expression profiling are biased by cross-hybridization of mouse-derived molecules to human probes. In addition, a reduction of sensitivity caused by measuring undesired mouse signals during nextgeneration sequencing analysis can be expected. To overcome these limitations, we developed a fast and easy method allowing for the effective depletion of all cells of mouse origin by using automated tissue dissociation and magnetic cell sorting (MACS® Technology). We performed whole exome sequencing (WES) of bulk human tumor xenografts from lung, bladder, and kidney cancer, and compared the results to samples depleted of mouse cells.