Detection of genetic or molecular aberrations associated with cancer

A method of analyzing a biological sample of an organism, the biological sample including nucleic acid molecules originating from normal cells and potentially from cells associated with cancer, wherein at least some of the nucleic acid molecules are cell-free in the biological sample, the method comprising:

• identifying a plurality of non-overlapping chromosomal regions of the organism, each chromosomal region including a plurality of loci;
• 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 a reference genome of the organism;
• for each of the plurality of non-overlapping chromosomal regions:
• identifying a respective group of nucleic acid molecules 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 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 respective reference value to determine a classification of whether the chromosomal region exhibits a deletion or an amplification;
• and
• determining an amount of chromosomal regions classified as exhibiting a deletion or amplification.