Sequencing analysis of circulating dna to detect and monitor autoimmune diseases

A method of analyzing a biological sample of an organism, the biological sample including nucleic acid molecules, wherein at least some of the nucleic acid molecules are cell-free, the method comprising:

• analyzing a plurality of DNA molecules from the biological sample, wherein analyzing a DNA molecule includes:
• determining whether the DNA molecule is methylated at one or more sites;
• calculating, with a computer system, a first methylation level based on the methylation determined at sites of the DNA molecules;
• comparing the first methylation level to a first reference value;
• and
• estimating a first level of an auto-immune disease in the organism based upon the comparison.

A method of analyzing a biological sample of an organism, the biological sample including nucleic acid molecules, wherein at least some of the nucleic acid molecules are cell-free, the method comprising:

• analyzing a plurality of DNA molecules from the biological sample, wherein analyzing a DNA molecule includes:
• determining a location of the DNA molecule in a genome of the organism;
• determining whether the DNA molecule is methylated at one or more sites;
• for each of a first plurality of genomic regions:
• determining, with a computer system, a methylation density at a plurality of sites in the genomic region based on the analysis of DNA molecules in the genomic region;
• comparing the methylation density to a first threshold to determine whether the region is hypomethylated;
• calculating a first amount of genomic regions that are hypomethylated;
• and
• estimating a level of an auto-immune disease in the organism based upon the first amount.

A method of analyzing a biological sample of an organism, the biological sample including nucleic acid molecules, wherein at least some of the nucleic acid molecules are cell-free, the method comprising:

• analyzing a plurality of DNA molecules from the biological sample, wherein analyzing a DNA molecule comprises:
• determining a size of the DNA molecule, and
• determining whether the DNA molecule is methylated at one or more sites;
• for a first size:
• calculating, with a computer system, a first methylation level based on the determined methylation for DNA molecules having the first size;
• comparing the first methylation level to a threshold methylation level;
• and
• estimating a level of an auto-immune disease in the organism based upon the comparison.

A method of analyzing a biological sample of an organism, the biological sample including nucleic acid molecules, wherein at least some of the nucleic acid molecules are cell-free, the method comprising:

• for each of a plurality of nucleic acid molecules from the biological sample, identifying a location of the nucleic acid molecule in a reference genome of the organism;
• for each of a plurality of genomic regions:
• identifying a respective group of nucleic acid molecules as being from the genomic region based on the identified locations;
• calculating, with a computer system, a respective value of the respective group of nucleic acid molecules, wherein the respective value defines a property of the nucleic acid molecules of the respective group;
• and
• comparing the respective value to a reference value to determine a classification of whether the genomic region exhibits an increased or decreased measured genomic representation;
• determining an amount of genomic regions classified as exhibiting an increased or decreased measured genomic representation;
• comparing the amount to a threshold amount;
• and
• estimating a first level of an auto-immune disease in the organism based upon the comparison.