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Updated: May 1, 2026
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Genome-Wide Analysis of DNA Methylation in Gastrointestinal Cancer
Published on: September 18, 2020
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DNA methylation microarray analysis of human DNA samples contaminated with mouse DNA
Takahiro Ebata1, Qichun Wang1, Hideyuki Takeshima1
1Department of Epigenomics, Institute for Advanced Life Sciences, Hoshi University, Tokyo, Japan.
Epigenomics
|April 30, 2026
Summary
This study developed a DNA methylation microarray method to accurately analyze human DNA, even with mouse DNA contamination. This technique improves the reliability of xenograft model studies.
Area of Science:
- Epigenetics and Genomics
- Bioanalytical Method Development
Background:
- Mouse DNA contamination is a significant challenge in analyzing human DNA from xenograft models.
- Existing methods struggle to accurately quantify human DNA methylation in the presence of xenogeneic DNA.
Purpose of the Study:
- To establish a DNA methylation microarray-based analytical method for human DNA.
- To specifically address and minimize interference from mouse DNA contamination.
Main Methods:
- Utilized the Infinium MethylationEPIC v2.0 kit for DNA methylation analysis.
- Generated and analyzed pure human DNA, mixtures with mouse DNA, and pure mouse DNA.
- Prepared cell line xenografts (CDX) from human cancer cell lines (RKO, Pa-Tu-8902).
Main Results:
- Identified and excluded 7,446 low-reproducibility human probes and 133,377 mouse cross-reacting probes.
- Exclusion of problematic probes significantly improved the correlation of methylation levels between pure human DNA and human-mouse DNA mixtures.
- Validated improved correlation for human CDX samples compared to their parental cell lines.
Conclusions:
- The developed method effectively minimizes mouse DNA contamination effects in human DNA samples.
- Enables more accurate analysis of human DNA methylation in both CDX and patient-derived xenograft (PDX) models.
- Facilitates reliable downstream applications using xenograft research models.
