Determining percentage of fetal DNA in maternal sample

A computer program product comprising a computer readable medium encoded with a plurality of instructions for controlling a measurement and computing system to perform a method of measuring a fractional concentration of fetal DNA in a biological sample of a female subject pregnant with a fetus, the biological sample including a mixture of cell-free nucleic acid molecules from the female subject and from the fetus, and wherein the female subject is homozygous at a first locus for a first allele and the fetus is heterozygous at the first locus for the first allele and a second allele different from the first allele, the method comprising:

• separating the cell-free nucleic acid molecules of the biological sample into a first plurality of reactions using a controller of the system;
• measuring, by a detector of the system, signals from the first plurality of reactions, each of the first plurality of reactions involving the first locus, wherein the signals are indicative of a presence or absence of the first allele and the second allele at the first locus in each of the first plurality of reactions;
• receiving, at a processor of the system, first data including the measured signals from the first plurality of reactions involving cell-free nucleic acid molecules from the biological sample, wherein the first data includes:
• (1) a first set of quantitative data indicating a first number of reactions positive for the first allele;
• and
• (2) a second set of quantitative data indicating a second number of reactions positive for the second allele;
• and
• comparing, by the processor of the system, the first number to the second number to measure the fractional concentration of fetal DNA.