US 11,926,821 B2
Cell-free DNA quality
Yuk-Ming Dennis Lo, Hong Kong SAR (CN); Cheuk Ho Tsang, Hong Kong SAR (CN); Peiyong Jiang, Hong Kong SAR (CN); Si Long Vong, Hong Kong SAR (CN); and Rossa Wai Kwun Chiu, Hong Kong SAR (CN)
Assigned to The Chinese University of Hong Kong, New Territories (HK)
Filed by The Chinese University of Hong Kong, New Territories (HK)
Filed on Oct. 21, 2019, as Appl. No. 16/658,677.
Claims priority of provisional application 62/748,767, filed on Oct. 22, 2018.
Prior Publication US 2020/0123532 A1, Apr. 23, 2020
Int. Cl. C12N 15/10 (2006.01); G16B 40/10 (2019.01); C40B 40/06 (2006.01); G16B 30/10 (2019.01); G16B 30/20 (2019.01); G16B 20/20 (2019.01); C12Q 1/6827 (2018.01); C12Q 1/6869 (2018.01); G16B 20/00 (2019.01); G16B 20/10 (2019.01); G16B 40/00 (2019.01)
CPC C12N 15/1065 (2013.01) [C12Q 1/6827 (2013.01); C12Q 1/6869 (2013.01); C40B 40/06 (2013.01); G16B 20/00 (2019.02); G16B 20/10 (2019.02); G16B 20/20 (2019.02); G16B 30/10 (2019.02); G16B 30/20 (2019.02); G16B 40/00 (2019.02); G16B 40/10 (2019.02)] 14 Claims
 
1. A method of determining an extent of cfDNA damage in an individual, the method comprising:
receiving a first sample comprising a first set of double-stranded nucleic acid molecules derived from cell-free nucleic acid molecules in a biological sample obtained from the individual, wherein:
one or more double-stranded nucleic acid molecules of the first set of double-stranded nucleic acid molecules each have one or more defects, and
the one or more defects are present in the respective double-stranded nucleic acid molecule at a location at least one nucleotide away from a closest end of the respective double-stranded nucleic acid molecule;
receiving a second sample comprising a second set of double-stranded nucleic acid molecules derived from the cell-free nucleic acid molecules in the biological sample;
adding a first mixture comprising an enzyme to the first sample;
adding a second mixture to the second sample, wherein the second mixture excludes the enzyme;
repairing the one or more defects in each of the one or more double-stranded nucleic acid molecules of the first set of double-stranded nucleic acid molecules using the enzyme to produce a repaired first set of double-stranded nucleic acid molecules, wherein the second set of double-stranded nucleic acid molecules is unrepaired;
sequencing the repaired first set of double-stranded nucleic acid molecules to determine a first set of reads;
sequencing the second set of double-stranded nucleic acid molecules to determine a second set of reads;
determining, based at least on sizes of the first set of reads and the second set of reads, a value of a parameter characterizing a difference in defects between the repaired first set of double-stranded nucleic acid molecules and the second set of double-stranded nucleic acid molecules;
comparing the value of the parameter to a reference value, wherein the reference value is determined using one or more healthy subjects; and
determining an extent of cfDNA damage for the individual based on the comparison of the value of the parameter to the reference value.