NON-INVASIVE DETERMINATION OF METHYLOME OF TUMOR FROM PLASMA
First Claim
1. 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:
- 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, by a computer system, whether the DNA molecule is methylated at one or more sites;
for each of a plurality of sites;
determining, by the computer system, a respective number of DNA molecules that are methylated at the site;
calculating, by the computer system, a first methylation level based on the respective numbers of DNA molecules methylated at the plurality of sites;
comparing the first methylation level to a first cutoff value; and
determining a first classification of a level of cancer based on the comparison.
1 Assignment
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Accused Products
Abstract
Systems, methods, and apparatuses can determine and use methylation profiles of various tissues and samples. Examples are provided. A methylation profile can be deduced for fetal/tumor tissue based on a comparison of plasma methylation (or other sample with cell-free DNA) to a methylation profile of the mother/patient. A methylation profile can be determined for fetal/tumor tissue using tissue-specific alleles to identify DNA from the fetus/tumor when the sample has a mixture of DNA. A methylation profile can be used to determine copy number variations in genome of a fetus/tumor. Methylation markers for a fetus have been identified via various techniques. The methylation profile can be determined by determining a size parameter of a size distribution of DNA fragments, where reference values for the size parameter can be used to determine methylation levels. Additionally, a methylation level can be used to determine a level of cancer.
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Citations
69 Claims
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1. 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:
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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, by a computer system, whether the DNA molecule is methylated at one or more sites; for each of a plurality of sites; determining, by the computer system, a respective number of DNA molecules that are methylated at the site; calculating, by the computer system, a first methylation level based on the respective numbers of DNA molecules methylated at the plurality of sites; comparing the first methylation level to a first cutoff value; and determining a first classification of a level of cancer based on the comparison. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68)
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69. A computer product comprising a non-transitory computer readable medium storing a plurality of instructions that when executed control a computer system to analyze 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 instructions comprising:
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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 plurality of sites; determining a respective number of DNA molecules that are methylated at the site; calculating a first methylation level based on the respective numbers of DNA molecules methylated at the plurality of sites; comparing the first methylation level to a first cutoff value; determining a first classification of a level of cancer based on the comparison.
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Specification