Non-invasive determination of methylome of tumor from plasma

1. A method of analyzing a biological sample of an organism, the biological sample comprising cell-free DNA originating from normal cells and potentially from cells associated with cancer, the method comprising:

analyzing a plurality of cell-free DNA molecules from the biological sample, wherein analyzing each of the plurality of cell-free DNA molecules includes:

determining a location of the cell-free DNA molecule in a genome of the organism; and

determining whether the cell-free DNA molecule is methylated at one or more sites, wherein determining whether the cell-free DNA molecule is methylated at the one or more sites comprises performing methylation-aware sequencing, and wherein performing methylation-aware sequencing comprises performing methylation-aware massively parallel sequencing, the one or more sites of each of the plurality of cell-free DNA molecules providing a plurality of sites;

for each site of the plurality of sites, individually counting a respective number of the cell-free DNA molecules at the site that are hypermethylated; and

calculating a first methylation level using the respective numbers of cell-free DNA molecules hypermethylated at the plurality of sites.

2. The method of claim 1 , wherein performing methylation-aware sequencing comprises sequencing of at least 60,000 cell-free DNA molecules.

3. The method of claim 1 , wherein performing methylation-aware sequencing generates between 39 million and 142 million reads.

4. The method of claim 1 , wherein performing methylation-aware sequencing includes:

treating the cell-free DNA molecules with sodium bisulfite; and

performing the methylation-aware massively parallel sequencing on the treated cell-free DNA molecules.

5. The method of claim 4 , wherein treating the cell-free DNA molecules with sodium bisulfite is part of Tet-assisted bisulfite conversion or oxidative bisulfite sequencing for a detection of 5-hydroxymethylcytosine.

6. The method of claim 1 , further comprising determining a first classification of a level of cancer based on the first methylation level.

7. The method of claim 6 , wherein determining the first classification of the level of cancer based on the first methylation level comprises:

comparing the first methylation level to a first cutoff value; and

determining the first classification of the level of cancer based on the comparison.

8. The method of claim 7 , wherein the first classification indicates that cancer exists for the organism, the method further comprising identifying a type of cancer associated with the organism by comparing the first methylation level to a corresponding value determined from other organisms, wherein at least two of the other organisms are identified as having different types of cancer.

9. The method of claim 7 , wherein the first cutoff value is a specified distance from a reference methylation level established from a biological sample obtained from a healthy organism.

10. The method of claim 9 , wherein the specified distance is a specified number of standard deviations from the reference methylation level.

11. The method of claim 7 , wherein the first cutoff value is established from a reference methylation level determined from a previous biological sample of the organism obtained previous to the biological sample being tested.

12. The method of claim 7 , wherein comparing the first methylation level to the first cutoff value includes:

determining a difference between the first methylation level and a reference methylation level; and

comparing the difference to a threshold corresponding to the first cutoff value.

13. The method of claim 7 , further comprising:

determining a fractional concentration of tumor DNA in the biological sample; and

calculating the first cutoff value based on the fractional concentration of tumor DNA in the biological sample.

14. The method of claim 7 , further comprising:

measuring a size of the cell-free DNA molecules at the plurality of sites, thereby obtaining measured sizes; and

before comparing the first methylation level to the first cutoff value, normalizing the first methylation level using cell-free DNA molecules having a first size.

15. The method of claim 14 , wherein the first size is a range of lengths.

16. The method of claim 14 , wherein the cell-free DNA molecules having the first size are selected based on a physical separation that is dependent on size.

17. The method of claim 14 , further comprising selecting the cell-free DNA molecules having the first size by:

performing paired-end massively parallel sequencing of the plurality of cell-free DNA molecules to obtain pairs of sequences for each of the cell-free DNA molecules;

determining a size of a cell-free DNA molecule by comparing the pair of sequences to a reference genome; and

selecting the cell-free DNA molecules having the first size.

18. The method of claim 14 , wherein normalizing the first methylation level using the cell-free DNA molecules having the first size includes:

obtaining a functional relationship between size and methylation levels; and

using the functional relationship to normalize the first methylation level, wherein the functional relationship provides scaling values corresponding to respective sizes.

19. The method of claim 18 , further comprising:

computing an average size corresponding to the cell-free DNA molecules used to calculate the first methylation level; and

multiplying the first methylation level by a corresponding scaling value.

20. The method of claim 18 , further comprising:

for each site of the plurality of sites:

for each of the cell-free DNA molecules located at the site:

obtaining a respective size of the cell-free DNA molecule at the site; and

using a scaling value corresponding to the respective size to normalize a contribution of the cell-free DNA molecule to the respective number of cell-free DNA molecules that are hypermethylated at the site.

21. The method of claim 7 , wherein the plurality of sites includes CpG sites, wherein the CpG sites are organized into a plurality of CpG islands, each CpG island including more than one CpG site, wherein the first methylation level corresponds to a first CpG island.

22. The method of claim 21 , further comprising:

for each CpG island of the plurality of CpG islands,

determining whether the CpG island is hypermethylated relative to a reference group of samples of other organisms by comparing a methylation level of the CpG island to a respective cutoff value, thereby determining hypermethylated CpG islands;

determining respective methylation densities for the hypermethylated CpG islands;

calculating a cumulative score from the respective methylation densities; and

comparing the cumulative score to a cumulative cutoff value to determine the first classification.

23. The method of claim 1 , further comprising:

determining whether a fractional concentration of tumor DNA in the biological sample is greater than a minimum value; and

if the fractional concentration of tumor DNA is not greater than the minimum value, flagging the biological sample.

24. The method of claim 23 , wherein the minimum value is determined based on an expected difference in methylation levels for a tumor relative to a reference methylation level.

25. The method of claim 1 , wherein the plurality of sites are on a plurality of chromosomes.

26. The method of claim 1 , wherein the plurality of sites are from disjointed regions separated from each other.

27. The method of claim 1 , wherein analyzing the plurality of cell-free DNA molecules comprises analyzing at least 10 million sequence reads.

28. A non-transitory computer readable medium comprising a plurality of instructions capable of execution by a computer system, that when so executed control the computer system to perform the method of claim 1 .