DNA methylation microarray analysis of human DNA samples contaminated with mouse DNA

AIM: To establish an analytical method for human DNA contamination with mouse DNA using a DNA methylation microarray. MATERIALS AND METHODS: A pure human DNA sample was generated by mixing fully methylated and unmethylated DNA originating from the human cell line HCT116 and fully methylated mouse DNA. The pure human DNA sample, human DNA samples mixed with 30% and 60% mouse DNA, and the pure mouse DNA samples were analyzed using the Infinium MethylationEPIC v2.0 kit. Cell line xenografts (CDX) were prepared from RKO and Pa-Tu-8902 cell lines. RESULTS: We identified 7,446 low-reproducibility probes using pure human DNA samples and 133,377 mouse cross-reacting probes using pure mouse DNA. After excluding these probes, functional probes improved the correlation in methylation levels between pure human DNA samples and those mixed with mouse DNA. Functional probes improved the correlation between DNA methylation levels in human CDX samples and their parental cancer cell lines. CONCLUSION: Our established method can minimize the effect of mouse DNA contamination in human DNA samples, thereby enabling the analysis of human CDX and patient-derived xenograft (PDX) models.