A method of analyzing a biological sample of an organism, the biological sample including DNA molecules originating from normal cells and potentially from cells associated with a non-hematopoietic cancer, the biological sample including cell-free DNA, the cell-free DNA including mitochondrial DNA and nuclear DNA, wherein the biological sample is plasma, the method comprising: receiving, at a computer system, sequence reads from a massively parallel sequencing of a plurality of DNA molecules from the biological sample of the organism; for each of a portion of the plurality of DNA molecules in the biological sample: identifying, by the computer system, whether the DNA molecule is a nuclear DNA molecule or a mitochondrial DNA molecule, including: determining a location of the DNA molecule in a reference nuclear genome that is non-repeat masked or a reference mitochondrial genome by attempting to map a corresponding sequence read to the reference nuclear genome and to the reference mitochondrial genome; and identifying whether the DNA molecule is a nuclear DNA molecule or a mitochondrial DNA molecule based on the location; measuring, by the computer system, a normalized amount of the plurality of DNA molecules that are identified as mitochondrial DNA molecules, wherein the normalized amount is a proportion of the plurality of DNA molecules that are mitochondrial DNA molecules in the biological sample; comparing, by the computer system, the normalized amount to a reference value; and determining, by the computer system, whether the non-hematopoietic cancer is in the organism based on the comparison, wherein the non-hematopoietic cancer is from non-hematopoietic cells that have higher number of mitochondria than hematopoietic cells, wherein the proportion of mitochondrial DNA molecules being higher than in healthy subjects indicates the non-hematopoietic cancer. receiving, at a computer system, sequence reads from a massively parallel sequencing of a plurality of DNA molecules from the biological sample of the organism; for each of a portion of the plurality of DNA molecules in the biological sample: identifying, by the computer system, whether the DNA molecule is a nuclear DNA molecule or a mitochondrial DNA molecule, including: determining a location of the DNA molecule in a reference nuclear genome that is non-repeat masked or a reference mitochondrial genome by attempting to map a corresponding sequence read to the reference nuclear genome and to the reference mitochondrial genome; and identifying whether the DNA molecule is a nuclear DNA molecule or a mitochondrial DNA molecule based on the location; determining a location of the DNA molecule in a reference nuclear genome that is non-repeat masked or a reference mitochondrial genome by attempting to map a corresponding sequence read to the reference nuclear genome and to the reference mitochondrial genome; and identifying whether the DNA molecule is a nuclear DNA molecule or a mitochondrial DNA molecule based on the location; measuring, by the computer system, a normalized amount of the plurality of DNA molecules that are identified as mitochondrial DNA molecules, wherein the normalized amount is a proportion of the plurality of DNA molecules that are mitochondrial DNA molecules in the biological sample; comparing, by the computer system, the normalized amount to a reference value; and determining, by the computer system, whether the non-hematopoietic cancer is in the organism based on the comparison, wherein the non-hematopoietic cancer is from non-hematopoietic cells that have higher number of mitochondria than hematopoietic cells, wherein the proportion of mitochondrial DNA molecules being higher than in healthy subjects indicates the non-hematopoietic cancer.