US 12,139,750 B2
Molecular analyses using long cell-free fragments in pregnancy
Yuk-Ming Dennis Lo, Hong Kong (CN); Rossa Wai Kwun Chiu, Hong Kong (CN); Kwan Chee Chan, Hong Kong (CN); Peiyong Jiang, Hong Kong (CN); Suk Hang Cheng, Hong Kong (CN); Cheuk Yin Yu, Hong Kong (CN); Yee Ting Cheung, Hong Kong (CN); and Wenlei Peng, Hong Kong (CN)
Assigned to The Chinese University of Hong Kong, New Territories (HK)
Filed by The Chinese University of Hong Kong, Shatin (HK)
Filed on Feb. 5, 2021, as Appl. No. 17/168,950.
Claims priority of provisional application 63/135,486, filed on Jan. 8, 2021.
Claims priority of provisional application 62/970,634, filed on Feb. 5, 2020.
Prior Publication US 2021/0265007 A1, Aug. 26, 2021
Int. Cl. C12Q 1/6827 (2018.01); C12Q 1/6806 (2018.01); C12Q 1/6881 (2018.01); C12Q 1/6883 (2018.01); G16B 20/20 (2019.01); G16B 30/10 (2019.01); G16B 40/00 (2019.01)
CPC C12Q 1/6827 (2013.01) [C12Q 1/6806 (2013.01); C12Q 1/6881 (2013.01); C12Q 1/6883 (2013.01); G16B 20/20 (2019.02); G16B 30/10 (2019.02); G16B 40/00 (2019.02); C12Q 2600/154 (2013.01)] 38 Claims
 
1. A method of analyzing a biological sample obtained from a female pregnant with a fetus, the biological sample including a plurality of cell-free DNA molecules from the fetus and the female, the method comprising:
receiving sequence reads corresponding to the plurality of cell-free DNA molecules;
measuring sizes of the plurality of cell-free DNA molecules;
identifying a set of cell-free DNA molecules from the plurality of cell-free DNA molecules as having sizes greater than or equal to a cutoff value, wherein the cutoff value is at least 500 nt; and
for a cell-free DNA molecule of the set of cell-free DNA molecules:
determining a methylation status at each site of a plurality of sites corresponding to the cell-free DNA molecule,
determining a methylation pattern using the methylation statuses, wherein:
the methylation pattern indicates a methylation status at each site of the plurality of sites, using one or more sequence reads corresponding to the cell-free DNA molecule,
comparing the methylation pattern to one or more reference patterns, wherein each of the one or more reference patterns is determined for a particular tissue type; and
determining a tissue of origin of the cell-free DNA molecule using the comparison.