Once recipient-specific markers have been found, quantification is performed to monitor engraftment. In the monitoring test, one or more of the informative assays is used to quantify the DNA of interest in an unknown sample relative to a reference sample. Any of the informative assays identified in the genotyping can be used to perform monitoring. The fraction of DNA positive for the informative marker in the unknown composition is determined relative to the pure reference sample DNA and the result is expressed as a percentage (ratio).