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.
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