The present invention provides a method for obtaining modified DNA from a biological specimen by obtaining a cell suspension from the specimen, if necessary; passing the cell suspension through a first filter under conditions sufficient to obtain filter-bound cells and suspended DNA; lysing the filter-bound cells under conditions sufficient to release cellular DNA; modifying the DNA bound to the filter under conditions sufficient to release the modified DNA from the filter into a flow-through volume; passing the flow-through volume through a second filter under conditions sufficient to capture the modified DNA to the second filter; and eluting the modified DNA from the second filter.