Molecular analyses using long cell-free fragments in pregnancy

A computer product comprising a non-transitory computer readable medium storing instructions that, when executed, control a computing system to perform 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 sizes of the plurality of cell-free DNA molecules;
• identifying a set of cell-free DNA molecules having sizes greater than a cutoff value, wherein the cutoff value is at least 500 nt;
• generating a value of an end motif parameter using a first amount, wherein generating the value of the end motif parameter comprises:
• receiving the first amount of cell-free DNA molecules in the set having a first subsequence at one or more ends of the cell-free DNA molecules in the set;
• comparing the value of the end motif parameter to a threshold value;
• and
• determining a classification of a likelihood of a pregnancy-associated disorder using the comparison.