ctDNA-based assays allow for the detection of minimal residual disease (MRD) earlier than standard clinical and imaging surveillance and could allow for treatment modification based on real-time assessment of the tumor genomic landscape. However, many challenges remain, as the analytical validation of liquid biopsy-based MRD assays requires reference materials allowing for the assessment of sensitivity and specificity at variant allele frequencies (VAFs) that can be over an order of magnitude below the typical limit of detection of standard ctDNA assays. At such low VAFs, there may be, on average, less than one copy of a somatic variant in a sample being analyzed out of billions of ctDNA fragments in a blood draw. This problem is why many MRD approaches use whole-exome sequencing data from patient tumors to design tumor-informed, personalized assays that target multiple patient-specific somatic variants, which reduces the amount of sequencing required to survey MRD while allowing the sequencing depth around the targeted variants to reach a level that is sufficient for high sensitivity and specificity.
This white paper from LGC SeraCare describes the creation of a reference material combining a tumor-derived component with a sufficiently large number of somatic mutations to accommodate the development, validation, and clinical deployment of custom, tumor-informed, ctDNA-based MRD monitoring assays.