Determining a nucleic acid sequence imbalance

A computer program product comprising a computer readable medium encoded with a plurality of instructions for controlling a computing system to perform an operation for determining whether a nucleic acid sequence imbalance exists within a biological sample of a female subject pregnant with at least one fetus, wherein the biological sample includes nucleic acid molecules from the female subject and from the at least one fetus, the instructions comprising:

• receiving data from a plurality of reactions involving nucleic acid molecules from the biological sample, wherein the data includes:
• (1) a first set of quantitative data indicating a first amount of a clinically relevant nucleic acid sequence in the plurality of reactions;
• and
• (2) a second set of quantitative data indicating a second amount of a background nucleic acid sequence in the plurality of reactions, the background nucleic acid sequence being different from the clinically relevant nucleic acid sequence;
• determining a parameter from the two data sets, wherein the parameter provides a numerical relationship between the first amount and the second amount;
• measuring an average concentration of a reference nucleic acid sequence in each of the plurality of reactions;
• deriving a first cutoff value from:
• the measured average concentration of a the reference nucleic acid sequence in each of the plurality of reactions, wherein the reference nucleic acid sequence is either the clinically relevant nucleic acid sequence or the background nucleic acid sequence, and
• an expected ratio between the clinically relevant nucleic acid sequence and the background nucleic acid sequence if a nucleic acid sequence imbalance exists, wherein deriving the first cutoff value includes:
• multiplying the measured average concentration and the expected ratio to obtain a second average concentration,
• determining a first probability of any reaction containing at least one reference nucleic acid sequence using the measured average concentration as an input to a probability distribution,
• determining a second probability of any reaction containing at least one of the non-reference nucleic acid sequence using the second average concentration as an input to the probability distribution, and
• calculating a ratio of the first probability and the second probability;
• comparing the parameter to the first cutoff value;
• and
• based on the comparison, determining a classification of whether the nucleic acid sequence imbalance exists.