Methods and compositions for detecting molecules in a heterogeneous sample are disclosed. The methods and compositions disclosed herein may be used for the treatment of a disease or condition characterized by the presence of nucleic acids from at least two different genomic sources. Additionally, the methods and compositions disclosed herein may be used to diagnose, predict, or monitor the status or outcome of a disease or condition characterized by the presence of nucleic acids from at least two different genomic sources. The heterogeneous samples may be from a transplant recipient, a chimeric individual, a subject suffering from a pathogenic infection, or a subject suffering from a different condition such as cancer.
