The present invention provides a method for preparing a preparation of amplified
DNA from a biological sample of a patient diagnosed with
cancer, useful for determining
cancer recurrence or
metastasis, comprising: (a) sequencing
DNA isolated from hematopoietic cells in the patient's blood or
bone marrow sample, or a fraction thereof, to determine the presence or absence of one or more clonal hematopoietic with undetermined potential (
CHIP) mutations; (b) sequencing (i)
DNA isolated from the patient's
tumor biopsy sample, or (ii)
cell-
free DNA isolated from the blood or
bone marrow sample, or a fraction thereof, to identify a plurality of patient-specific somatic mutations associated with the
cancer; and (c) sequencing the
cell-
free DNA isolated from the patient's longitudinally collected biological sample, or a fraction thereof, to identify a plurality of patient-specific somatic mutations associated with the cancer. The present invention provides a method comprising: preparing a preparation of amplified DNA by performing a
multiplex amplification to amplify a plurality of target loci to obtain amplified DNA, wherein each of the target loci spans a patient-specific somatic
mutation identified in step (b) and does not span any of the
CHIP mutations identified in step (a), and the biological sample is a blood,
urine, or
bone marrow sample; and (d) analyzing the preparation of amplified DNA by sequencing the amplified DNA to determine the presence or absence of the patient-specific somatic mutations, wherein the presence of two or more patient-specific somatic mutations associated with cancer and the presence of one or more
CHIP mutations is indicative of
cancer recurrence or
metastasis.