A single-molecule epistate approach for understanding tumor epigenomes

Ben Berman
University of Southern California (USC)

Whole-genome bisulfite sequencing (WGBS) can be used to construct a comprehensive map of the epigenetic states in a patient tumor sample. While WGBS is a popular technique, current computational analysis methods fail to exploit its unique single-molecule properties. We have developed a new method, single-molecule epistate analysis, which takes as input two or more tumor WGBS samples, and uses these single-molecule patterns to identify epigenetic state changes genome-wide. Because the algorithm operates at the level of individual DNA molecule, it can be used to identify epigenetic state changes occurring within specific subpopulations of cells within a tumor sample. We will demonstrate results of this method using sequence data we have produced for dozens of tumors as part of NIH’s The Cancer Genome Atlas (TCGA) project.

Back to Translating Cancer Data and Models to Clinical Practice