Methylation pattern analysis of haplotypes in tissues in a dna mixture

A computer product comprising a non-transitory computer readable medium storing a plurality of instructions for analyzing a biological sample of an organism, the biological sample including a mixture of cell-free DNA molecules from a plurality of tissues types, including a first tissue type, wherein the plurality of instructions, when executed, cause one or more processors of a computer system to perform:

• analyzing a plurality of cell-free DNA molecules from the biological sample, the plurality of cell-free DNA molecules being at least 1,000 cell-free DNA molecules, wherein analyzing a cell-free DNA molecule includes:
• identifying a location of the cell-free DNA molecule in a reference genome corresponding to the organism;
• determining a respective allele of the cell-free DNA molecule;
• identifying one or more loci, each having a corresponding first allele on a first haplotype of a first chromosomal region, wherein the first haplotype is:
• not present in healthy cells of the organism, or
• present in the healthy cells of the organism and not present in abnormal cells that may be in the mixture;
• identifying a first set of the plurality of cell-free DNA molecules that each:
• is located at any one locus of the one or more loci,
• includes the corresponding first allele of the one locus, and
• includes at least one of N genomic sites, N being an integer greater than or equal to 2;
• measuring N first mixture methylation levels at the N genomic sites using the first set of the plurality of cell-free DNA molecules;
• determining a first fractional contribution of the first tissue type in the mixture using the N first mixture methylation levels;
• determining a first separation value between the first fractional contribution and a reference fractional contribution;
• and
• comparing the first separation value to a threshold value to determine a classification of whether the first tissue type has a disease state.

A system for analyzing a biological sample of an organism, the biological sample including a mixture of cell-free DNA molecules from a plurality of tissues types, including a first tissue type, the system comprising:

• an apparatus configured to perform an assay on a plurality of cell-free DNA molecules from the biological sample to provide measurement data, the plurality of cell-free DNA molecules being at least 1,000 cell-free DNA molecules;
• a computer system configured to receive the measurement data and to perform:
• analyzing the plurality of cell-free DNA molecules from the biological sample, wherein analyzing a cell-free DNA molecule includes:
• identifying a location of the cell-free DNA molecule in a reference genome corresponding to the organism;
• determining a respective allele of the cell-free DNA molecule;
• identifying one or more loci, each having a corresponding first allele on a first haplotype of a first chromosomal region, wherein the first haplotype is:
• not present in healthy cells of the organism, or
• present in the healthy cells of the organism and not present in abnormal cells that may be in the mixture;
• identifying a first set of the plurality of cell-free DNA molecules that each:
• is located at any one locus of the one or more loci,
• includes the corresponding first allele of the one locus, and
• includes at least one of N genomic sites, N being an integer greater than or equal to 2;
• measuring N first mixture methylation levels at the N genomic sites using the first set of the plurality of cell-free DNA molecules;
• determining a first fractional contribution of the first tissue type in the mixture using the N first mixture methylation levels;
• determining a first separation value between the first fractional contribution and a reference fractional contribution;
• and
• comparing the first separation value to a threshold value to determine a classification of whether the first tissue type has a disease state.