A method of determining a progress of chromosomal aberrations in an organism using biological samples including nucleic acid molecules originating from normal cells and potentially from cells associated with a cancer, wherein at least some of the nucleic acid molecules are cell-free in the biological samples, the method comprising: a. identifying one or more non-overlapping chromosomal regions of a reference genome of the organism, each chromosomal region including a plurality of loci; b. at each of a plurality of times: i. for each of a plurality of nucleic acid molecules in a biological sample of the organism, identifying a location of the nucleic acid molecule in the reference genome; ii. for each of the one or more non-overlapping chromosomal regions: identifying a respective group of nucleic acid molecules within the plurality of nucleic acid molecules as being from the chromosomal region based on the identified locations, the respective group of nucleic acid molecules including at least one nucleic acid molecule located at each of the plurality of loci of the chromosomal region; calculating, with a computer system, a respective value of the respective group of nucleic acid molecules, the respective value defining a property of the nucleic acid molecules of the respective group; and comparing the respective value to a reference value to determine a classification of whether the chromosomal region exhibits a deletion or an amplification; and c. using the one or more classifications of the one or more non-overlapping chromosomal regions at the plurality of times to determine the progress of the chromosomal aberrations in the organism, wherein using the one or more classifications comprises: calculating a numerical change from the classification at one time to the classification at another time; and comparing the numerical change to a threshold value. a. identifying one or more non-overlapping chromosomal regions of a reference genome of the organism, each chromosomal region including a plurality of loci; b. at each of a plurality of times: i. for each of a plurality of nucleic acid molecules in a biological sample of the organism, identifying a location of the nucleic acid molecule in the reference genome; ii. for each of the one or more non-overlapping chromosomal regions: identifying a respective group of nucleic acid molecules within the plurality of nucleic acid molecules as being from the chromosomal region based on the identified locations, the respective group of nucleic acid molecules including at least one nucleic acid molecule located at each of the plurality of loci of the chromosomal region; calculating, with a computer system, a respective value of the respective group of nucleic acid molecules, the respective value defining a property of the nucleic acid molecules of the respective group; and comparing the respective value to a reference value to determine a classification of whether the chromosomal region exhibits a deletion or an amplification; and i. for each of a plurality of nucleic acid molecules in a biological sample of the organism, identifying a location of the nucleic acid molecule in the reference genome; ii. for each of the one or more non-overlapping chromosomal regions: identifying a respective group of nucleic acid molecules within the plurality of nucleic acid molecules as being from the chromosomal region based on the identified locations, the respective group of nucleic acid molecules including at least one nucleic acid molecule located at each of the plurality of loci of the chromosomal region; calculating, with a computer system, a respective value of the respective group of nucleic acid molecules, the respective value defining a property of the nucleic acid molecules of the respective group; and comparing the respective value to a reference value to determine a classification of whether the chromosomal region exhibits a deletion or an amplification; and identifying a respective group of nucleic acid molecules within the plurality of nucleic acid molecules as being from the chromosomal region based on the identified locations, the respective group of nucleic acid molecules including at least one nucleic acid molecule located at each of the plurality of loci of the chromosomal region; calculating, with a computer system, a respective value of the respective group of nucleic acid molecules, the respective value defining a property of the nucleic acid molecules of the respective group; and comparing the respective value to a reference value to determine a classification of whether the chromosomal region exhibits a deletion or an amplification; and c. using the one or more classifications of the one or more non-overlapping chromosomal regions at the plurality of times to determine the progress of the chromosomal aberrations in the organism, wherein using the one or more classifications comprises: calculating a numerical change from the classification at one time to the classification at another time; and comparing the numerical change to a threshold value. calculating a numerical change from the classification at one time to the classification at another time; and comparing the numerical change to a threshold value.