Using test patterns of chromosomal regions in plasma dna for detecting 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 chromosomal regions of the organism, each chromosomal region including a plurality of loci, wherein the plurality of chromosomal regions are subchromosomal;
• for each of a plurality of nucleic acid molecules in the 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 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 a test pattern of the chromosomal regions that exhibit a deletion or amplification, the test pattern including:
• a set of the chromosomal regions that exhibit a deletion or amplification;
• a first subset of the set that exhibit an amplification;
• and
• a second subset of the set that exhibit a deletion;
• comparing the test pattern to a plurality of reference patterns of different types of cancer;
• based on the comparison, determining a first amount of regions of the test pattern that exhibit a same deletion or amplification as a first reference pattern corresponding to a first type of cancer;
• and
• comparing the first amount to a first threshold to determine a first classification of whether the biological sample exhibits the first type of cancer.