A computer-implemented method of analyzing a biological sample of an organism, the biological sample including nucleic acid molecules originating from normal cells and from cells derived from tumor tissue, wherein at least some of the nucleic acid molecules are cell-free in the biological sample, the method comprising: identifying a plurality of chromosomal regions of the organism, each chromosomal region including a plurality of loci and resulting from a splitting of a chromosome into a plurality of regions, wherein the plurality of chromosomal regions is non-overlapping, and wherein a first chromosomal region is one of the plurality of chromosomal regions; for each of the plurality of the nucleic acid molecules in the biological sample: measuring a size of the nucleic acid molecule; identifying a location of the nucleic acid molecule in a reference genome of the organism; for each of the plurality of chromosomal regions: identifying a respective group of a plurality of nucleic acid molecules in the biological sample as being from the chromosomal region based on the identified locations, the respective group 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 amount of the respective group of nucleic acid molecules; and comparing the respective amount to a count reference value to determine a count classification of whether the chromosomal region exhibits an aberration, the aberration being a copy number aberration, the count classification indicating a first aberration for the first chromosomal region of the plurality of chromosomal regions; identifying a first group of nucleic acid molecules from the sample as being from the first chromosomal region based on the identified locations; calculating, with a computer system, a first statistical value of a first size distribution of the first group of nucleic acid molecules; comparing the first statistical value to a size reference value to determine a size classification of whether the first chromosomal region exhibits the first aberration.; and determining a final classification of whether the first chromosomal region exhibits the first aberration using the count classification and the size classification of the first chromosomal region. identifying a plurality of chromosomal regions of the organism, each chromosomal region including a plurality of loci and resulting from a splitting of a chromosome into a plurality of regions, wherein the plurality of chromosomal regions is non-overlapping, and wherein a first chromosomal region is one of the plurality of chromosomal regions; for each of the plurality of the nucleic acid molecules in the biological sample: measuring a size of the nucleic acid molecule; identifying a location of the nucleic acid molecule in a reference genome of the organism; measuring a size of the nucleic acid molecule; identifying a location of the nucleic acid molecule in a reference genome of the organism; for each of the plurality of chromosomal regions: identifying a respective group of a plurality of nucleic acid molecules in the biological sample as being from the chromosomal region based on the identified locations, the respective group 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 amount of the respective group of nucleic acid molecules; and comparing the respective amount to a count reference value to determine a count classification of whether the chromosomal region exhibits an aberration, the aberration being a copy number aberration, the count classification indicating a first aberration for the first chromosomal region of the plurality of chromosomal regions; identifying a respective group of a plurality of nucleic acid molecules in the biological sample as being from the chromosomal region based on the identified locations, the respective group 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 amount of the respective group of nucleic acid molecules; and comparing the respective amount to a count reference value to determine a count classification of whether the chromosomal region exhibits an aberration, the aberration being a copy number aberration, the count classification indicating a first aberration for the first chromosomal region of the plurality of chromosomal regions; identifying a first group of nucleic acid molecules from the sample as being from the first chromosomal region based on the identified locations; calculating, with a computer system, a first statistical value of a first size distribution of the first group of nucleic acid molecules; comparing the first statistical value to a size reference value to determine a size classification of whether the first chromosomal region exhibits the first aberration.; and determining a final classification of whether the first chromosomal region exhibits the first aberration using the count classification and the size classification of the first chromosomal region.