	US 11,984,195 B2
	Methylation pattern analysis of tissues in a DNA mixture
Rossa Wai Kwun Chiu, Shatin (CN); Kwan Chee Chan, Shatin (CN); Yuk-Ming Dennis Lo, Homantin (CN); Peiyong Jiang, Shatin (CN); and Kun Sun, Shatin (HK)
Assigned to The Chinese University of Hong Kong, Shatin (HK)
Filed by The Chinese University of Hong Kong, Shatin (HK)
Filed on Oct. 15, 2018, as Appl. No. 16/160,951.
Application 16/160,951 is a division of application No. 14/803,692, filed on Jul. 20, 2015, granted, now 11,062,789.
Claims priority of provisional application 62/183,669, filed on Jun. 23, 2015.
Claims priority of provisional application 62/158,466, filed on May 7, 2015.
Claims priority of provisional application 62/026,330, filed on Jul. 18, 2014.
Prior Publication US 2019/0050528 A1, Feb. 14, 2019
Int. Cl. C12Q 1/6809 (2018.01); C12Q 1/689 (2018.01); G16B 20/00 (2019.01); G16B 20/10 (2019.01); G16B 20/20 (2019.01); G16B 30/10 (2019.01); G16B 30/00 (2019.01)

CPC G16B 20/20 (2019.02) [C12Q 1/6809 (2013.01); C12Q 1/689 (2013.01); G16B 20/00 (2019.02); G16B 20/10 (2019.02); G16B 30/10 (2019.02); C12Q 2600/112 (2013.01); C12Q 2600/154 (2013.01); G16B 30/00 (2019.02)]

29 Claims

1. A method of analyzing a biological sample of an organism, the biological sample including a mixture of cell-free DNA molecules from M tissues types, M being greater than two, the method comprising:

identifying N genomic sites, wherein, for one or more other samples, a first set of the N genomic sites each have a coefficient of variation of methylation levels of at least 0.15 across the M tissue types and each have a difference between a maximum and a minimum methylation level for the M tissue types that exceeds 0.1, the first set including at least 10 genomic sites;

for each of the M tissue types:

obtaining N tissue-specific methylation levels at the N genomic sites, N being greater than or equal to M, wherein the tissue-specific methylation levels form a matrix A of dimensions N by M;

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 each of the plurality of cell-free DNA molecules includes:

identifying a location of the cell-free DNA molecule in a reference genome corresponding to the organism, wherein locations of a number of the plurality of cell-free DNA molecules that depends on N for a given accuracy are identified;

measuring N mixture methylation levels at the N genomic sites using a first group of the plurality of cell-free DNA molecules that are each located at any one of N genomic sites of the reference genome corresponding to the organism, wherein the N mixture methylation levels form a methylation vector b;

solving for a composition vector x that provides the methylation vector b for the matrix A; and

for each of one or more components of the composition vector x:

using the component to determine an amount of a corresponding tissue type of the M tissue types in the mixture.