A method of analyzing a biological sample of an organism, the biological sample including DNA fragments originating from normal cells and potentially from cells associated with cancer, wherein at least some of the DNA fragments are cell-free in the biological sample, the method comprising: for each of a plurality of DNA fragments from the biological sample: receiving one or more sequence reads obtained from a sequencing of the DNA fragment, the one or more sequence reads including both ends of the DNA fragment; aligning the one or more sequence reads to a reference genome to obtain aligned locations for both ends of the DNA fragment; and using the aligned locations to determine a size of the DNA fragment; for each size of a plurality of sizes: determining an amount of a first set of the plurality of DNA fragments from the biological sample corresponding to the size using the sizes determined from the aligned locations for the first set; calculating a first value of a first parameter based on the amounts of DNA fragments at multiple sizes, the first parameter providing a statistical measure of a size profile of DNA fragments in the biological sample; comparing the first value to a reference value; and determining a classification of a level of cancer in the organism based on the comparison. for each of a plurality of DNA fragments from the biological sample: receiving one or more sequence reads obtained from a sequencing of the DNA fragment, the one or more sequence reads including both ends of the DNA fragment; aligning the one or more sequence reads to a reference genome to obtain aligned locations for both ends of the DNA fragment; and using the aligned locations to determine a size of the DNA fragment; for each size of a plurality of sizes: determining an amount of a first set of the plurality of DNA fragments from the biological sample corresponding to the size using the sizes determined from the aligned locations for the first set; calculating a first value of a first parameter based on the amounts of DNA fragments at multiple sizes, the first parameter providing a statistical measure of a size profile of DNA fragments in the biological sample; comparing the first value to a reference value; and determining a classification of a level of cancer in the organism based on the comparison. receiving one or more sequence reads obtained from a sequencing of the DNA fragment, the one or more sequence reads including both ends of the DNA fragment; aligning the one or more sequence reads to a reference genome to obtain aligned locations for both ends of the DNA fragment; and using the aligned locations to determine a size of the DNA fragment; for each size of a plurality of sizes: determining an amount of a first set of the plurality of DNA fragments from the biological sample corresponding to the size using the sizes determined from the aligned locations for the first set; calculating a first value of a first parameter based on the amounts of DNA fragments at multiple sizes, the first parameter providing a statistical measure of a size profile of DNA fragments in the biological sample; comparing the first value to a reference value; and determining a classification of a level of cancer in the organism based on the comparison. determining an amount of a first set of the plurality of DNA fragments from the biological sample corresponding to the size using the sizes determined from the aligned locations for the first set; calculating a first value of a first parameter based on the amounts of DNA fragments at multiple sizes, the first parameter providing a statistical measure of a size profile of DNA fragments in the biological sample; comparing the first value to a reference value; and determining a classification of a level of cancer in the organism based on the comparison.