cfDNA reference material, for example, for use in verifying the accuracy and effectiveness of a diagnostic test, is generated from chromatin which may be sourced from whole cells. The chromatin may be treated with formaldehyde to form crosslinks between DNA and histones, for example, while the chromatin is contained within nuclear and/or plasma membranes. The fixed chromatin may be sheared by acoustic energy, which may also be used to lyse cell membranes within which the fixed chromatin may be contained. The sheared chromatin may be treated with an enzyme, such as micrococcal nuclease, to digest chromatin in linker regions of the DNA between nucleosomes and generate nucleosome material for use as cfDNA reference material.